X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details sodium acetate, PEG 300, DTT , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.88 α = 90
b = 83.88 β = 90
c = 94.34 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 double crystal Si 111 monochromator 2002-05-02
Diffraction Radiation
Monochromator Protocol
double crystal Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 1.033 SSRL BL1-5

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
2.7 30 99.8 0.141 0.141 -- 2.1 20337 20139 0.0 0.0 53.112
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)
2.7 2.8 99.4 0.35 0.35 2.0 2.1 2035

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
FOURIER SYNTHESIS 2.7 20.0 -- 0.0 19324 19096 979 98.82 0.155 0.1553 0.15243 0.21134 copied from test set for 1OXN
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 2.7 2.769 1376 72 1376 0.209 0.273 -- 99.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.175
Anisotropic B[1][1] 0.66
Anisotropic B[1][2] 0.33
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.008
r_symmetry_hbond_refined 0.18
r_scangle_it 6.421
r_chiral_restr 0.081
r_nbd_refined 0.21
r_xyhbond_nbd_refined 0.15
r_symmetry_vdw_refined 0.18
r_angle_refined_deg 1.079
r_dihedral_angle_1_deg 5.141
r_mcbond_it 3.057
r_scbond_it 3.908
r_gen_planes_refined 0.004
r_mcangle_it 5.379
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3980
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 403

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
SCALEPACK data scaling
CNS phasing