Experiment: 3B9D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B9E	PDB ENTRY 3B9E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	288	16% (w/v) PEG 4000, 0.1M magnesium chloride, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.508	α = 90
b = 83.076	β = 90
c = 105.586	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	IMAGE PLATE	RIGAKU RAXIS IV++		2006-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.72	24.54	99.2	0.071	0.077	26.3	6.8	59561	59561			17.2

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	1.72	1.81	95.6		0.123	0.136	9.9	5.6	8247

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 3B9E	1.72	24.54	59561	56474	3024	99.16	0.18841	0.18841	0.18703	0.2145	RANDOM	15.683

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]
-0.2			-0.19		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.291
r_dihedral_angle_3_deg	12.033
r_dihedral_angle_4_deg	9.327
r_dihedral_angle_1_deg	5.146
r_scangle_it	1.337
r_angle_refined_deg	0.962
r_scbond_it	0.923
r_mcangle_it	0.648
r_mcbond_it	0.491
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.291
r_dihedral_angle_3_deg	12.033
r_dihedral_angle_4_deg	9.327
r_dihedral_angle_1_deg	5.146
r_scangle_it	1.337
r_angle_refined_deg	0.962
r_scbond_it	0.923
r_mcangle_it	0.648
r_mcbond_it	0.491
r_nbtor_refined	0.302
r_nbd_refined	0.17
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.129
r_xyhbond_nbd_refined	0.087
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4353
Nucleic Acid Atoms
Solvent Atoms	664
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

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.