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 = 83.19 α = 90
b = 83.19 β = 90
c = 93.61 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 MARRESEARCH -- 2002-04-13
Diffraction Radiation
Monochromator Protocol
unknown SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 32-ID 1.2686 APS 32-ID

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 20 97.2 0.065 0.065 -- 3.7 64496 62709 0.0 0.0 41.211
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 0.379 0.379 3.4 3.9 6453

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 2.3 20.0 -- 0.0 30570 29677 1528 97.08 0.1634 0.16345 0.16064 0.21827 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 2.3 2.359 -- 117 2169 0.221 0.273 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.259
Anisotropic B[1][1] 0.28
Anisotropic B[1][2] 0.14
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 6.082
r_chiral_restr 0.074
r_symmetry_hbond_refined 0.166
r_scbond_it 3.994
r_gen_planes_refined 0.004
r_nbd_refined 0.204
r_mcangle_it 5.347
r_xyhbond_nbd_refined 0.142
r_symmetry_vdw_refined 0.174
r_mcbond_it 3.193
r_bond_refined_d 0.009
r_angle_refined_deg 1.073
r_dihedral_angle_1_deg 4.976
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3979
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