X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 50 mM Imidazole, pH 7.5 350 mM Sodium Acetate 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.49 α = 90
b = 79.17 β = 105.58
c = 54.89 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 RIGAKU SATURN 92 Viramax 2006-04-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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 50 99.1 0.086 -- -- 3.3 25984 24384 -3.0 0.0 10.6
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)
2.1 2.18 93.7 0.255 -- 3.07 -- --

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 22.11 -- 0.0 25984 24384 2404 93.0 0.2 0.198 0.198 0.252 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 -- 392 3458 0.24 0.31 0.016 88.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.0
Anisotropic B[1][1] 1.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.16
Anisotropic B[2][2] 0.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.4
c_improper_angle_d 1.69
c_mcangle_it 2.41
c_angle_deg 1.1
c_mcbond_it 1.47
c_scangle_it 3.01
c_bond_d 0.005
c_scbond_it 2.02
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2626
Nucleic Acid Atoms 633
Heterogen Atoms 4
Solvent Atoms 487

Software

Software
Software Name Purpose
HKL-2000 data collection
CNS refinement
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing