X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.8
Temperature 292.0
Details PEG 6K, KCl, Na-acetate, NH4Cl, MgCl2, pH 5.8, VAPOR DIFFUSION, 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 monochromator 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 20 -- 0.15 0.15 -- 6.0 366365 366365 -3.0 -3.0 39.9
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)
3.0 3.11 95.2 0.709 0.709 2.3 4.0 34695

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 19.99 0.0 0.0 359798 337448 3303 92.9 0.219 0.219 0.219 0.262 RANDOM same 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 -- 290 28404 0.334 0.361 0.021 79.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 55.1
Anisotropic B[1][1] 12.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.2
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.99
c_scbond_it 1.24
c_mcangle_it 1.81
c_mcbond_it 1.05
c_improper_angle_d 1.6
c_bond_d 0.009
c_angle_deg 1.3
c_dihedral_angle_d 17.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28801
Nucleic Acid Atoms 61617
Heterogen Atoms 298
Solvent Atoms 7877

Software

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