Experiment: 1WVP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A6K	PDB ENTRY 1A6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7	293	Ammonium Sulfate, Phosphate, pH 7.0, batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.982	α = 90
b = 60.982	β = 90
c = 84.808	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	IMAGE PLATE	RIGAKU RAXIS V		2003-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.53	50	98.9	0.05	45.95		24645	24611			16.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.53	1.58	97.9		0.345	9.37		2366

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 1A6K	1.53	20	23316	23316	1242	99.02	0.175	0.175	0.174	0.208	RANDOM	19.043

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]
-0.45			-0.45		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.02
r_scangle_it	4.898
r_sphericity_free	3.868
r_sphericity_bonded	3.579
r_scbond_it	3.268
r_mcangle_it	2.396
r_rigid_bond_restr	1.645
r_angle_refined_deg	1.549
r_mcbond_it	1.513
r_nbd_refined	0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.02
r_scangle_it	4.898
r_sphericity_free	3.868
r_sphericity_bonded	3.579
r_scbond_it	3.268
r_mcangle_it	2.396
r_rigid_bond_restr	1.645
r_angle_refined_deg	1.549
r_mcbond_it	1.513
r_nbd_refined	0.26
r_symmetry_hbond_refined	0.203
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.161
r_chiral_restr	0.096
r_metal_ion_refined	0.073
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1249
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
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.