X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 290.0
Details AMMONIUM SULFATE, MAGNESIUM SULFATE, MPD, MES, MANGANESE SULFATE, pH 5.80, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.68 α = 90
b = 91.68 β = 90
c = 190.12 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRROR 2001-03-29
Diffraction Radiation
Monochromator Protocol
Si Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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 39.7 99.8 0.062 -- -- 4.9 129531 129531 -- -3.0 23.2
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 2.02 99.3 0.48 -- 2.5 4.1 12800

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 1.95 39.7 -- 2.0 98839 96536 4574 74.2 0.264 0.218 0.218 0.261 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 -- 259 4895 0.307 0.332 0.021 39.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 43.9
Anisotropic B[1][1] 0.3
Anisotropic B[1][2] 0.74
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.6
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.26
c_scbond_it 0.83
c_mcangle_it 1.12
c_mcbond_it 0.66
c_improper_angle_d 1.42
c_dihedral_angle_d 23.2
c_angle_deg 1.3
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9294
Nucleic Acid Atoms 974
Heterogen Atoms 69
Solvent Atoms 186

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection