3KHK

Crystal structure of type-I restriction-modification system methylation subunit (MM_0429) from Methanosarchina mazei.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 298.0
Details Sodium acetate trihydrate pH 4.6, 25% PEG 3350,0.2M Ammonium Acetate,0.05M Magnesium Sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.65 α = 90
b = 80.65 β = 90
c = 179.97 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-20
CCD ADSC QUANTUM 315 -- 2009-03-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C

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
2.5 25 100.0 0.098 0.117 -- 10.6 37205 37205 -- -- --
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)
2.55 2.59 100.0 0.816 0.882 3.0 10.7 1916

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
SAD 2.55 25.0 -- 0.0 -- 37097 1858 99.65 -- 0.214 0.213 0.242 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 2.553 2.619 -- 123 2542 0.244 0.381 -- 97.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.862
Anisotropic B[1][1] 5.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.64
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.287
r_dihedral_angle_4_deg 19.83
r_gen_planes_refined 0.005
r_scbond_it 1.424
r_dihedral_angle_2_deg 40.963
r_chiral_restr 0.097
r_mcangle_it 1.018
r_angle_refined_deg 1.355
r_scangle_it 2.204
r_mcbond_it 0.545
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 6.458
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7863
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 18

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
CBASS data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing
SHELXD phasing