Experiment: 3C08

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L7I	PDB id 1L7I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	1.8M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.821	α = 90
b = 61.377	β = 90
c = 102.675	γ = 90

Symmetry
Space Group	P 21 21 21

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 210		2007-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.918	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	52.7	99.9	0.102	0.102	7.2	5.3	20191	20191

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23	99.9		0.417	0.417	3.618	4.6	1971

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 id 1L7I	2.15	50	20127	20127	1029	99.2	0.226	0.226	0.224	0.264	RANDOM	25.434

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]
-1.2			1.35		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.502
r_dihedral_angle_4_deg	18.367
r_dihedral_angle_1_deg	18.277
r_dihedral_angle_3_deg	17.007
r_scangle_it	1.885
r_angle_refined_deg	1.329
r_mcangle_it	1.297
r_scbond_it	1.19
r_mcbond_it	0.832
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.502
r_dihedral_angle_4_deg	18.367
r_dihedral_angle_1_deg	18.277
r_dihedral_angle_3_deg	17.007
r_scangle_it	1.885
r_angle_refined_deg	1.329
r_mcangle_it	1.297
r_scbond_it	1.19
r_mcbond_it	0.832
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.218
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.107
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3097
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.