4Q52 | pdb_00004q52

2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	protein: 7.8 mg/mL in 10 mM Tris/HCl, 500 mM NaCl, 5 mM BME crystallization: the PACT Suite (C11: 0.2 M CaCl2, 0.1 M HEPES pH 7.0, 20 % (w/v) PEG 6000) cryo: 25 % glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.712	α = 90
b = 85.549	β = 104.19
c = 88.195	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	MARMOSAIC 225 mm CCD	Be lenses	2014-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	30	99.9	0.152	0.152	12.2	4.8	22847	22847		-3	44.1

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	2.6	2.64	100		0.641	2.5	4.8	1110

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.6	29.19	21649	21649	1167	99.53	0.17114	0.16869	0.1761	0.21529	0.2161	RANDOM	34.912

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]
0.43		0.64	-2.67		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	33.075
r_dihedral_angle_2_deg	30.116
r_dihedral_angle_3_deg	12.377
r_dihedral_angle_1_deg	4.539
r_angle_refined_deg	1.62
r_angle_other_deg	1.057
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	33.075
r_dihedral_angle_2_deg	30.116
r_dihedral_angle_3_deg	12.377
r_dihedral_angle_1_deg	4.539
r_angle_refined_deg	1.62
r_angle_other_deg	1.057
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5306
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	36

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.