X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.0
Details PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.4 α = 90
b = 109.7 β = 97.8
c = 40 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2000-03-22
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.00 APS 14-BM-C

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
2.15 500 96.6 0.048 -- -- 2.66 28101 24648 0.0 0.0 51.8
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)
2.15 2.19 92.4 0.465 -- 2.37 2.16 1277

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 2.15 19.96 0.0 0.0 28101 24648 2437 88.4 0.238 0.238 0.232 0.29 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 2.15 2.28 -- 337 2879 0.417 0.426 0.023 69.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 50.02
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 13.9
Anisotropic B[2][2] -3.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.56
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.93
c_scbond_it 2.03
c_mcangle_it 2.57
c_mcbond_it 1.58
c_improper_angle_d 0.77
c_dihedral_angle_d 25.0
c_angle_deg 1.29824
c_bond_d 0.006381
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2382
Nucleic Acid Atoms 1328
Heterogen Atoms 5
Solvent Atoms 168

Software

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