X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 0.2M zinc acetate, 0.1M imidazole, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.09 α = 90
b = 71.85 β = 90
c = 118.14 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-11-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C -- APS 24-ID-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
2 34.6 99.0 0.062 -- -- 6.9 -- 15537 -- -- --
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)
2.0 2.07 95.5 0.335 -- -- 5.6 1465

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
SAD 2.0 34.6 -- 0.0 -- 15537 776 98.46 -- 0.196 0.194 0.229 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 1.995 2.047 1002 38 964 0.204 0.198 -- 87.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.035
Anisotropic B[1][1] -0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.47
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.081
r_symmetry_vdw_refined 0.282
r_xyhbond_nbd_refined 0.175
r_gen_planes_refined 0.005
r_metal_ion_refined 0.279
r_dihedral_angle_1_deg 4.32
r_symmetry_metal_ion_refined 0.103
r_symmetry_hbond_refined 0.173
r_dihedral_angle_4_deg 16.967
r_nbd_refined 0.21
r_mcbond_it 0.646
r_mcangle_it 1.211
r_scangle_it 3.117
r_scbond_it 1.941
r_dihedral_angle_3_deg 14.437
r_bond_refined_d 0.012
r_angle_refined_deg 1.091
r_dihedral_angle_2_deg 33.179
r_nbtor_refined 0.298
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1352
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 118

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
SHARP phasing