2ZQE

Crystal structure of the Smr domain of Thermus thermophilus MutS2


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.5
Temperature 293.0
Details 0.1M Citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.81 α = 90
b = 54.22 β = 90
c = 30.24 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2008-04-11
Diffraction Radiation
Monochromator Protocol
transparent diamond double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2

Data Collection

Overall
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
1.7 50 99.8 0.047 -- -- 6.3 -- 9284 -- -- 11.8
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.76 99.8 0.137 -- 13.1 6.3 58499

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.7 7.9 -- -- -- 8597 443 100.0 -- 0.19074 0.18876 0.22699 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.702 1.744 -- 24 597 0.19 0.291 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.168
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.302
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 4.9
r_scangle_it 3.982
r_chiral_restr 0.066
r_dihedral_angle_2_deg 36.456
r_scbond_it 2.296
r_dihedral_angle_4_deg 7.149
r_dihedral_angle_3_deg 11.44
r_nbd_refined 0.198
r_symmetry_hbond_refined 0.172
r_angle_refined_deg 1.066
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.147
r_mcangle_it 1.204
r_symmetry_vdw_refined 0.116
r_mcbond_it 0.676
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 599
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 104

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing