Experiment: 4Y99

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Dimethy sulfoxide

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.062	α = 90
b = 80.368	β = 90
c = 93.712	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	CCD	RIGAKU JUPITER 210		2006-12-09	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	70	97.2	0.063	21.8	7		31896

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	2.07	83.2		0.351	5.9	5.9

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	1J1D	2	50	31896	1680	97.04	0.2317	0.2302	0.2588	RANDOM	46.459

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]
-0.14			-2.71		2.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.538
r_dihedral_angle_4_deg	21.113
r_dihedral_angle_3_deg	12.823
r_scangle_it	4.384
r_dihedral_angle_1_deg	4.235
r_scbond_it	2.438
r_mcangle_it	1.477
r_angle_refined_deg	0.971
r_mcbond_it	0.732
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.538
r_dihedral_angle_4_deg	21.113
r_dihedral_angle_3_deg	12.823
r_scangle_it	4.384
r_dihedral_angle_1_deg	4.235
r_scbond_it	2.438
r_mcangle_it	1.477
r_angle_refined_deg	0.971
r_mcbond_it	0.732
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2871
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	27

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	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 R01GM133198.