4HB5 | pdb_00004hb5

Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR267.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GPM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch crystallization under oil	8	277	20% PEG 4000, 0.1M magnesium sulfate, 0.1M Tris-HCl, pH 8.0, Microbatch crystallization under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.977	α = 90
b = 45.469	β = 107.17
c = 63.152	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	CCD	MAR CCD 165 mm		2012-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97885	NSLS	X4C

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	2.3	50	98.9	0.071	24.5	3.7	27096	26798			28.07

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	2.3	2.37	99.9		0.146	8.8	3.8	2694

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	4GPM	2.294	35.537	1.15	26546	1316	97.99	0.196	0.194	0.19	0.236	0.23	RANDOM	39.025

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]
-1.868		5.09	-10.693		12.561

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.113
f_angle_d	1.375
f_chiral_restr	0.09
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2419
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.