X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 291.0
Details 1 mM sodium citrate, 10% acetone, 15 mM nickel(II) acetate tetrahydrate, pH 6.4, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.41 α = 90
b = 81.41 β = 90
c = 33.75 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-10-28
Diffraction Radiation
Monochromator Protocol
The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R

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
1.35 16.41 99.7 -- -- -- -- 29352 18240 -- -- --
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)
1.35 1.385 100.0 -- -- -- -- --

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
-- 1.35 16.41 -- 0.0 18240 18240 935 99.7 0.126 0.126 0.124 0.171 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 1.35 1.385 -- 63 1277 0.13 0.227 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.198
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 7.482
r_sphericity_free 10.719
r_rigid_bond_restr 2.93
r_bond_refined_d 0.028
r_angle_refined_deg 2.15
r_dihedral_angle_1_deg 21.571
r_dihedral_angle_2_deg 34.246
r_dihedral_angle_3_deg 13.042
r_dihedral_angle_4_deg 9.224
r_chiral_restr 0.17
r_gen_planes_refined 0.013
r_mcbond_it 2.778
r_mcangle_it 3.891
r_scbond_it 5.041
r_scangle_it 6.722
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 810
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 151

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC 5.4.0067 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 version: 5.4.0067 refinement
SCALA data processing
Mosflm collection/data indexing