X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 4.0
Details 50 mM MES, pH 6.6, 200 mM NaCl, 50 mM MgCl2, 6-8% PEG3350 and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.48 α = 90
b = 168.8 β = 90
c = 238.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirros 2000-11-29
Diffraction Radiation
Monochromator Protocol
mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 1.0 APS 14-BM-D

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
2.8 52 94.6 0.085 0.085 -- 4.4 131998 124870 0.0 0.0 64.6
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)
2.8 2.98 88.8 0.47 0.47 -- 4.0 18358

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 2.8 51.79 0.0 0.0 131998 124870 6267 94.6 0.233 0.233 0.233 0.272 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 2.8 2.98 -- 949 18358 0.36 0.401 0.013 88.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 57.2
Anisotropic B[1][1] 2.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -11.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.25
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 8.45
c_scbond_it 6.27
c_mcangle_it 4.09
c_mcbond_it 2.49
c_improper_angle_d 1.49
c_dihedral_angle_d 26.3
c_angle_deg 1.7
c_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 30870
Nucleic Acid Atoms 0
Heterogen Atoms 168
Solvent Atoms 428

Software

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