3C2Q | pdb_00003c2q

Crystal structure of conserved putative LOR/SDH protein from Methanococcus maripaludis S2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	1.00M Sodium citrate, 0.10M Imidazole pH 8.0, 0.05M Sodium fluoride, cryoprotected with 25% v/v Glycerol and saturated Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.592	α = 90
b = 119.592	β = 90
c = 161.737	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	SBC-3	Mirrors	2007-08-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979229	APS	19-BM

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	100	93.3	0.056		7.4	80188	75521		2

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)
	2	2.1	99.7		0.252	6.2	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MAD	THROUGHOUT	2	96.23	3	75521	74815	3994	99.78	0.19215	0.19086	0.1929	0.21694	0.2197	RANDOM	27.514

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			0.14		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.302
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_4_deg	12.906
r_dihedral_angle_1_deg	8.19
r_scangle_it	5.014
r_scbond_it	3.503
r_mcangle_it	1.732
r_angle_refined_deg	1.479
r_mcbond_it	1.328
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.302
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_4_deg	12.906
r_dihedral_angle_1_deg	8.19
r_scangle_it	5.014
r_scbond_it	3.503
r_mcangle_it	1.732
r_angle_refined_deg	1.479
r_mcbond_it	1.328
r_nbtor_refined	0.302
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.176
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5045
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	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.