2OYN | pdb_00002oyn

Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	100mM Hepes pH 7.5, 10% Isopropanol, 17% PEG 4000, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.48	α = 90
b = 63.48	β = 90
c = 73.117	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	MAR CCD 165 mm		2007-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.85	47.946	99.9	0.137	0.137	26.6	27.9	13339	13339			22.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	100		0.866	0.866	4.6	28.1	1907

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	1.85	20	13294	13294	656	99.98	0.199	0.197	0.2	0.239	0.24	RANDOM	26.034

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]
-0.19			-0.19		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.843
r_dihedral_angle_4_deg	12.95
r_dihedral_angle_3_deg	12.867
r_dihedral_angle_1_deg	5.526
r_scangle_it	4.295
r_scbond_it	2.686
r_mcangle_it	1.717
r_angle_refined_deg	1.646
r_mcbond_it	0.922
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.843
r_dihedral_angle_4_deg	12.95
r_dihedral_angle_3_deg	12.867
r_dihedral_angle_1_deg	5.526
r_scangle_it	4.295
r_scbond_it	2.686
r_mcangle_it	1.717
r_angle_refined_deg	1.646
r_mcbond_it	0.922
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.115
r_metal_ion_refined	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1113
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	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.