X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.97 α = 90
b = 34.97 β = 90
c = 64.24 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2002-01-10
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
1.45 30 99.3 0.034 -- -- 7.1 4525 4525 -- -2.0 --
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)
1.45 1.5 94.2 0.135 -- 10.5 -- --

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 1.45 30.29 0.0 0.0 4496 4053 443 99.38 -- 0.18884 0.18535 0.22388 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 1.45 1.488 -- 30 262 0.248 0.259 -- 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 12.368
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.22
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.254
r_dihedral_angle_1_deg 3.116
r_chiral_restr 0.051
r_mcbond_it 0.681
r_scbond_it 2.418
r_angle_other_deg 0.733
r_gen_planes_refined 0.004
r_xyhbond_nbd_refined 0.293
r_scangle_it 4.26
r_metal_ion_refined 0.205
r_symmetry_hbond_refined 0.28
r_symmetry_vdw_other 0.142
r_mcangle_it 1.34
r_angle_refined_deg 1.365
r_bond_refined_d 0.008
r_symmetry_vdw_refined 0.341
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_nbd_refined 0.346
r_nbtor_other 0.087
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 157
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 26

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing