X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PEG 3350, sodium HEPES, Calcium Chloride, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.53 α = 90
b = 99.32 β = 90
c = 113.89 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 mirror 2001-11-30
CCD SBC-1 mirror 2001-11-26
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) MAD
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.96411, 0.97939, 0.9795 APS 19-BM
SYNCHROTRON APS BEAMLINE 19-ID 1.0719 APS 19-ID

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
1.7 43.14 97.4 0.074 -- -- 5.5 53243 53243 0.0 0.0 14.6
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)
1.7 1.76 81.6 0.244 -- 2.6 2.1 4407

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 1.7 43.14 -- 0.0 51727 51727 5224 93.3 0.226 0.226 0.224 0.246 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 1.7 1.81 -- 667 6162 0.296 0.305 0.012 74.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 17.5
Anisotropic B[1][1] -1.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.04
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.4
c_mcbond_it 1.65
c_scbond_it 2.85
c_angle_deg 1.4
c_improper_angle_d 0.88
c_mcangle_it 2.2
c_scangle_it 4.05
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3576
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 437

Software

Computing
Computing Package Purpose
CRYSTALCLEAR D*STREK (MSC/RIGAKU), HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
CNS model building
CNS version: 1.0 refinement
d*streck/HKL2000 data collection