Experiment: 2R87

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R7K	PDB entry 2R7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	291	10% 2-propanol, 200 mM Li2SO4, 100 mM Na phosphate-citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.095	α = 90
b = 127.222	β = 102.85
c = 121.673	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 270		2007-01-01	M	SINGLE WAVELENGTH
2	1		IMAGE PLATE	RIGAKU RAXIS IV		2007-05-05

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91770	CHESS	F1
2	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	50	98.8	0.138	8.7	4.4	98989	98928

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	98.5		0.264		2.9	9860

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2R7K	2.3	42.64	98989	98928	4941	98.67	0.203	0.203	0.201	0.244	RANDOM	22.251

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.37		-1.66			-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.627
r_dihedral_angle_3_deg	14.87
r_dihedral_angle_4_deg	9.23
r_dihedral_angle_1_deg	5.711
r_scangle_it	1.414
r_angle_refined_deg	1.067
r_scbond_it	0.827
r_mcangle_it	0.735
r_mcbond_it	0.419
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.627
r_dihedral_angle_3_deg	14.87
r_dihedral_angle_4_deg	9.23
r_dihedral_angle_1_deg	5.711
r_scangle_it	1.414
r_angle_refined_deg	1.067
r_scbond_it	0.827
r_mcangle_it	0.735
r_mcbond_it	0.419
r_nbtor_refined	0.302
r_nbd_refined	0.175
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.098
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16230
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	257

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.