X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 299.0
Details PEGMME 5000, Tris, NaCl, Ca.ATP, EDTA, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.6 α = 80.6
b = 78.4 β = 76.9
c = 135 γ = 71.8
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2000-03-17
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator, Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.008 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
2.1 40 96.3 -- 0.058 -- 3.7 -- 150398 -- -- 19.0
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)
2.1 2.18 92.0 -- 0.373 2.8 3.6 14381

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 20.0 -- 0.0 149733 142899 14256 91.9 0.235 0.222 0.222 0.259 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 19216 2100 -- 0.289 0.34 0.007 82.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 34.2
Anisotropic B[1][1] 4.03
Anisotropic B[1][2] 1.83
Anisotropic B[1][3] -0.7
Anisotropic B[2][2] 0.74
Anisotropic B[2][3] -0.42
Anisotropic B[3][3] -4.78
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.5
c_dihedral_angle_d 24.3
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18531
Nucleic Acid Atoms 0
Heterogen Atoms 264
Solvent Atoms 665

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
EPMR model building
SCALEPACK data reduction
HKL-2000 data collection