Experiment: 3VN4

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	20% PEG1500, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.378	α = 90
b = 53.243	β = 111.56
c = 76.615	γ = 90

Symmetry
Space Group	C 1 2 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 315		2011-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	2.8	50	99.1	0.048	20.3	3.7	14407	14278

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	2.8	2.9	99		0.31	6.28	3.7	1405

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	PDB ENTRY 3GHM	2.8	30.93	13674	13509	738	98.79	0.232	0.232	0.229	0.23	0.277	0.23	RANDOM	62.369

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]
-2.99		-3.66	2.48		-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.703
r_dihedral_angle_4_deg	14.882
r_dihedral_angle_3_deg	13.985
r_dihedral_angle_1_deg	5.237
r_scangle_it	1.691
r_angle_refined_deg	0.95
r_scbond_it	0.95
r_angle_other_deg	0.736
r_mcangle_it	0.666
r_mcbond_it	0.348

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.703
r_dihedral_angle_4_deg	14.882
r_dihedral_angle_3_deg	13.985
r_dihedral_angle_1_deg	5.237
r_scangle_it	1.691
r_angle_refined_deg	0.95
r_scbond_it	0.95
r_angle_other_deg	0.736
r_mcangle_it	0.666
r_mcbond_it	0.348
r_chiral_restr	0.055
r_mcbond_other	0.033
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2894
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	74

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
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.