X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 292.0
Details PEG 6K, KCl, NH4Cl, KOAc MgCl2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 212.9 α = 90
b = 300.47 β = 90
c = 575.18 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2000-09-27
Diffraction Radiation
Monochromator Protocol
Si 111 Si 220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.033 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
3 50 99.2 0.136 0.136 -- 7.2 370864 367880 -3.0 -3.0 44.0
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)
2.98 3.09 94.8 0.816 0.816 2.0 34384.0 36270

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 3.0 20.0 0.0 0.0 364257 339428 3311 93.3 0.227 0.227 0.227 0.265 RANDOM same r-free set as 1JJ2
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 3.0 3.11 -- 286 28711 0.348 0.363 0.021 80.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.6
Anisotropic B[1][1] 7.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.81
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.0
c_mcangle_it 1.82
c_angle_deg 1.4
c_mcbond_it 1.04
c_bond_d 0.009
c_dihedral_angle_d 17.7
c_scbond_it 1.25
c_improper_angle_d 1.62
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.55
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28801
Nucleic Acid Atoms 61617
Heterogen Atoms 292
Solvent Atoms 7850

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing