3C1L | pdb_00003c1l

Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	NANODROP, 20.0% PEG 6000, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	6.2	277	NANODROP, 0.2M NaCl, 50.0% PEG 200, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.69	α = 90
b = 68.06	β = 95.94
c = 266.83	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 325 mm CCD	Flat mirror (vertical focusing)	2007-02-11	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837	SSRL	BL11-1
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97942	APS	23-ID-D

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	2	29.814	84.6	0.058	7.38			138837		-3	21.909

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	2	2.07	41.9		0.354	1.6

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	SAD + MOLECULAR REPLACEMENT	THROUGHOUT	2	29.814	138822	6959	87.53	0.174	0.171	0.18	0.225	0.23	RANDOM	24.95

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]
-0.31		-0.04	0.25		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.995
r_dihedral_angle_3_deg	15.072
r_dihedral_angle_4_deg	13.86
r_scangle_it	5.879
r_dihedral_angle_1_deg	5.846
r_scbond_it	4.223
r_mcangle_it	2.248
r_angle_refined_deg	1.498
r_mcbond_it	1.466
r_angle_other_deg	0.992

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.995
r_dihedral_angle_3_deg	15.072
r_dihedral_angle_4_deg	13.86
r_scangle_it	5.879
r_dihedral_angle_1_deg	5.846
r_scbond_it	4.223
r_mcangle_it	2.248
r_angle_refined_deg	1.498
r_mcbond_it	1.466
r_angle_other_deg	0.992
r_mcbond_other	0.711
r_chiral_restr	0.087
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	16600
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOSFLM	data reduction
XSCALE	data scaling
SCALA	data scaling
SHARP	phasing
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.