Experiment: 2DDB

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	3.6M sodium formate, 10%(w/v) glycerol, 0.15M NaCl, 50mM Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.707	α = 90
b = 61.668	β = 90
c = 251.224	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		2003-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6B	1.0000	Photon Factory	BL-6B

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	1.9	50	98.5	0.109	4.7	6.2		74335			21.7

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	1.9	1.97	100		0.315	2.1	7.2	7454

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1WVR	1.9	43.27	74329	3745	100	0.209	0.206	0.258	RANDOM	26.737

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.542
r_dihedral_angle_4_deg	16.273
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_1_deg	5.489
r_scangle_it	2.445
r_scbond_it	1.537
r_angle_refined_deg	1.173
r_mcangle_it	1.078
r_mcbond_it	0.581
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.542
r_dihedral_angle_4_deg	16.273
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_1_deg	5.489
r_scangle_it	2.445
r_scbond_it	1.537
r_angle_refined_deg	1.173
r_mcangle_it	1.078
r_mcbond_it	0.581
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.254
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.159
r_metal_ion_refined	0.111
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6532
Nucleic Acid Atoms
Solvent Atoms	721
Heterogen Atoms	103

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.