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_scangle_it 4.26
r_scbond_it 2.418
r_mcangle_it 1.34
r_mcbond_it 0.681
r_symmetry_hbond_refined 0.28
r_symmetry_vdw_other 0.142
r_symmetry_vdw_refined 0.341
r_metal_ion_refined 0.205
r_bond_refined_d 0.008
r_bond_other_d 0.002
r_angle_refined_deg 1.365
r_angle_other_deg 0.733
r_dihedral_angle_1_deg 3.116
r_chiral_restr 0.051
r_gen_planes_refined 0.004
r_gen_planes_other 0.002
r_nbd_refined 0.346
r_nbd_other 0.254
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.293
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement