X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details 0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.88 α = 90
b = 105.88 β = 90
c = 105.88 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-02-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C

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
1.96 25.68 99.6 0.081 -- -- 42.9 -- 28616 -- -- --
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)
1.96 2.01 100.0 0.902 -- -- 43.1 --

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 1.96 25.68 -- -- -- 27141 1448 99.58 -- 0.1882 0.18569 0.23611 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 1.96 2.01 -- 101 1986 0.201 0.29 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.133
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.271
r_dihedral_angle_2_deg 38.892
r_xyhbond_nbd_other 0.103
r_bond_refined_d 0.023
r_dihedral_angle_1_deg 6.573
r_angle_refined_deg 1.885
r_gen_planes_other 0.003
r_scbond_it 2.923
r_gen_planes_refined 0.009
r_nbtor_other 0.089
r_bond_other_d 0.002
r_angle_other_deg 1.008
r_nbd_refined 0.246
r_dihedral_angle_3_deg 16.208
r_symmetry_metal_ion_refined 0.046
r_nbtor_refined 0.175
r_scangle_it 4.225
r_chiral_restr 0.128
r_mcangle_it 1.634
r_symmetry_hbond_refined 0.238
r_metal_ion_refined 0.195
r_symmetry_vdw_refined 0.378
r_mcbond_other 0.348
r_symmetry_vdw_other 0.291
r_dihedral_angle_4_deg 19.941
r_nbd_other 0.206
r_xyhbond_nbd_refined 0.211
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2404
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 209

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data scaling