Experiment: 3WVB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WVA	SeMet-labelled HcgF PDB ENTRY 3WVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	20%(w/v)PEG3000, 200mM sodium chloride, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.31	α = 90
b = 73.11	β = 102.22
c = 45.53	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	PIXEL	PSI PILATUS 6M		2011-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.270	SLS	X10SA

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	1.7	50	98.6	0.023	39.88	3.62		31585		-3	21.029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8	96.8		0.042	0.05	25.62

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SeMet-labelled HcgF PDB ENTRY 3WVA	1.7	44.28	31563	1600	98.81	0.1476	0.1452	0.1908	RANDOM	14.677

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]
0.01		-0.01	0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.798
r_dihedral_angle_4_deg	24.353
r_dihedral_angle_3_deg	14.922
r_dihedral_angle_1_deg	5.936
r_scbond_it	2.363
r_angle_refined_deg	2.286
r_mcangle_it	1.357
r_mcbond_it	0.926
r_chiral_restr	0.19
r_bond_refined_d	0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.798
r_dihedral_angle_4_deg	24.353
r_dihedral_angle_3_deg	14.922
r_dihedral_angle_1_deg	5.936
r_scbond_it	2.363
r_angle_refined_deg	2.286
r_mcangle_it	1.357
r_mcbond_it	0.926
r_chiral_restr	0.19
r_bond_refined_d	0.022
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2668
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
MOLREP	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.