X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.3
Temperature 298.0
Details PEG3350, Calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.74 α = 90
b = 50.11 β = 97.53
c = 89.61 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 -- 2002-11-25
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9065 SPRING-8 BL12B2

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
2.3 40 100.0 -- 0.073 -- 7.5 21213 21165 0.0 0.0 19.5
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)
2.3 2.38 100.0 -- 0.282 4.4 -- --

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 2.3 19.78 -- 0.0 21279 20729 1616 97.5 -- -- 0.191 0.26 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 2.3 2.44 -- 264 3025 0.201 0.263 0.016 953.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.4
Anisotropic B[1][1] 6.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.92
Anisotropic B[2][2] -0.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.47
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.04
c_scbond_it 2.09
c_mcangle_it 2.29
c_mcbond_it 1.45
c_improper_angle_d 1.14
c_dihedral_angle_d 21.8
c_angle_deg 1.4
c_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3450
Nucleic Acid Atoms 645
Heterogen Atoms 2
Solvent Atoms 328

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