X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 295.0
Details PEG 4000, sodium cholride, sodium citrate, EDTA, 2-mercaptoethanol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.91 α = 90
b = 98.91 β = 90
c = 98.91 γ = 90
Symmetry
Space Group P 42 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.00000 Photon Factory BL-6A

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
2.5 44 100.0 -- 0.086 -- 38.0 6146 6146 0.0 0.0 53.5
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)
2.5 2.64 100.0 -- 0.484 -- -- --

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 2.6 19.78 -- 2.0 5469 5133 558 93.8 -- 0.218 0.218 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 2.6 2.76 -- 77 642 0.338 0.397 0.045 81.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 52.2
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.009
c_mcbond_it 4.51
c_scbond_it 7.11
c_mcangle_it 6.53
c_improper_angle_d 0.85
c_scangle_it 8.6
c_angle_deg 1.4
c_dihedral_angle_d 23.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.49
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1221
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 19

Software

Software
Software Name Purpose
CNS refinement version: 1.1
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
CNS phasing