3F7C | pdb_00003f7c

Crystal structure of a duf416 family protein (maqu_0942) from marinobacter aquaeolei vt8 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	277	1.0M sodium citrate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.998	α = 90
b = 76.998	β = 90
c = 91.26	γ = 120

Symmetry
Space Group	P 64

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645,0.97967	APS	23-ID-B

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	29.424	100	0.089	0.089	4.107	7.4		20811			37.979

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	2	2.05	99.8		0.835	0.835	0.9	5.7	1510

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2	29.424	20774	1067	99.92	0.173	0.172	0.17	0.196	0.19	RANDOM	35.327

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]
-0.13	-0.06		-0.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.655
r_dihedral_angle_3_deg	12.881
r_dihedral_angle_4_deg	12.81
r_scangle_it	7.903
r_scbond_it	5.51
r_dihedral_angle_1_deg	4.904
r_mcangle_it	3.142
r_mcbond_it	1.884
r_angle_refined_deg	1.503
r_angle_other_deg	0.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.655
r_dihedral_angle_3_deg	12.881
r_dihedral_angle_4_deg	12.81
r_scangle_it	7.903
r_scbond_it	5.51
r_dihedral_angle_1_deg	4.904
r_mcangle_it	3.142
r_mcbond_it	1.884
r_angle_refined_deg	1.503
r_angle_other_deg	0.926
r_mcbond_other	0.553
r_chiral_restr	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1564
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.