X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details Tris, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.44 α = 90
b = 125.44 β = 90
c = 72.34 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Diamond (111), Ge(220) 2003-02-01
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9322 ESRF ID14-1

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
1.85 19.83 99.9 0.083 0.083 -- 3.4 108560 108560 0.0 0.0 20.98
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)
1.85 1.95 99.7 0.474 0.474 1.8 3.1 15302

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 1.85 19.84 0.0 0.0 103138 103138 5422 100.0 0.19771 0.19771 0.19522 0.24381 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 1.85 1.898 -- 400 7617 0.266 0.31 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, Zn atoms anisotropic
Mean Isotropic B 27.257
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.022
r_metal_ion_refined 0.402
r_scbond_it 3.334
r_scangle_it 4.911
r_angle_refined_deg 1.901
r_dihedral_angle_1_deg 7.397
r_mcangle_it 2.247
r_chiral_restr 0.148
r_gen_planes_refined 0.01
r_mcbond_it 1.323
r_nbd_refined 0.316
r_symmetry_vdw_refined 0.517
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7770
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 877

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.80
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MOLREP phasing