X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details HEPES, PEG6000, glycerol, manganese chloride, DL-isocitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.4 α = 90
b = 119.02 β = 99.01
c = 128.22 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-09-20
Diffraction Radiation
Monochromator Protocol
MIRROR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9000 SPring-8 BL41XU

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
1.95 20 98.9 0.083 0.071 -- 3.6 237767 235314 -- 3.0 24.474
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)
1.95 2.06 96.7 0.388 0.327 2.0 3.2 33505

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
MAD, Molecular Replacement method 1.95 10.0 -- 0.0 233612 235314 23269 98.9 -- -- 0.193 0.228 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 1.95 2.02 22769 2325 20444 0.2254 0.264 -- 96.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic for overall
Mean Isotropic B 23.5096
Anisotropic B[1][1] -3.913
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.92
Anisotropic B[2][2] 3.002
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.911
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 1.16
c_scangle_it 2.79
c_scbond_it 1.96
c_angle_deg 1.22762
c_dihedral_angle_d 21.6516
c_mcangle_it 1.68
c_bond_d 0.00494
c_improper_angle_d 0.82829
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22586
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 2306

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SHARP phasing
SHELXS phasing
AMoRE phasing
DM model building
DMMulti model building
CNS refinement
CCP4 data scaling version: (SCALA)
DM phasing
DMMulti phasing