X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 20.0
Details 1.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.25 α = 90
b = 64.25 β = 90
c = 195.48 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-12
Diffraction Radiation
Monochromator Protocol
Silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.936 ESRF ID29

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
2.1 19.73 98.9 -- 0.087 -- 5.7 27942 27942 0.0 -3.0 33.6
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)
2.1 2.21 100.0 -- 0.297 2.3 6.0 4064

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 2.1 19.71 -- 0.0 27887 27887 1353 98.7 0.216 0.215 0.215 0.243 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 2.1 2.23 4394 228 4394 0.218 0.262 0.017 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.7
Anisotropic B[1][1] 3.64
Anisotropic B[1][2] 3.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.27
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 4.88
c_mcbond_it 3.43
c_scangle_it 6.05
c_dihedral_angle_d 21.1
c_bond_d 0.008
c_angle_deg 1.4
c_mcangle_it 5.23
c_improper_angle_d 0.99
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2915
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 237

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
CNS refinement version: 1.0
CCP4 data scaling version: (SCALA)
CNS phasing version: 1.0