Experiment: 4NBR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SJ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	JCSG+(e1): 1M Sodium Citrate Tribasic, 0.1M Sodium Cacodylate/HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.76	α = 90
b = 76.62	β = 90
c = 87.6	γ = 90

Symmetry
Space Group	I 2 2 2

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	MARMOSAIC 225 mm CCD	Beryllium Lenses	2013-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	.97857	APS	21-ID-F

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	1.35	50	99.9	0.054	19.27	5.9	53242	53190		-3	18.05

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)
1	1.35	1.39	99.9		0.452	2.91

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3SJ7	1.35	50	55891	53189	2702	99.9	0.102	0.102	0.1004	0.1	0.1332	0.13	RANDOM	15.711

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]
-0.4			-0.13		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.331
r_sphericity_free	31.768
r_dihedral_angle_4_deg	14.563
r_dihedral_angle_3_deg	10.849
r_sphericity_bonded	8.453
r_dihedral_angle_1_deg	5.917
r_rigid_bond_restr	2.67
r_mcangle_it	1.846
r_mcbond_it	1.505
r_mcbond_other	1.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.331
r_sphericity_free	31.768
r_dihedral_angle_4_deg	14.563
r_dihedral_angle_3_deg	10.849
r_sphericity_bonded	8.453
r_dihedral_angle_1_deg	5.917
r_rigid_bond_restr	2.67
r_mcangle_it	1.846
r_mcbond_it	1.505
r_mcbond_other	1.505
r_angle_refined_deg	1.473
r_angle_other_deg	0.848
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1977
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.