X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.74 α = 90
b = 94.74 β = 90
c = 159.9 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirror 2000-04-12
CCD MARRESEARCH mirror 2000-03-25
Diffraction Radiation
Monochromator Protocol
si 111 SINGLE WAVELENGTH
si 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.9326 ESRF ID14-2
SYNCHROTRON ESRF BEAMLINE BM14 1.7389,1.7401,0.9918 ESRF BM14

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
2.8 28 97.7 0.038 0.038 -- 4.6 17823 17423 0.0 0.0 79.0
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)
2.8 2.9 99.8 0.36 0.36 2.1 4.7 1718

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 2.83 19.91 0.0 0.0 17823 17382 841 96.6 0.286 0.286 0.282 0.296 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 2.8 2.97 1659 94 2290 0.457 0.538 0.055 79.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 106.9
Anisotropic B[1][1] 7.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.46
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.23
c_scbond_it 1.86
c_dihedral_angle_d 26.4
c_mcangle_it 4.18
c_bond_d 0.021
c_angle_deg 2.4
c_mcbond_it 2.52
c_improper_angle_d 2.39
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.55
Luzzati Sigma A (Observed) 0.7
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.57
Luzzati Sigma A (R-Free Set) 0.66
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4032
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 330

Software

Software
Software Name Purpose
MLPHARE phasing
CNS refinement version: 0.9
DENZO data reduction
CCP4 data scaling version: (SCALA)