X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details Tris.HCl, sodium formate, glycerol, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 206.05 α = 90
b = 206.05 β = 90
c = 292.86 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
2 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-12-23
CCD CUSTOM-MADE -- 2002-07-21
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal MAD
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-ID
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9611, 0.9797, 0.98, 1.00348 APS 14-BM-D

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
2.4 95.35 98.1 -- 0.089 -- -- 139810 139810 -3.0 -3.0 --
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)
2.4 2.49 98.2 -- 0.483 -- -- 13803

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
MAD 2.601 95.35 -- 1.0 -- 105541 5631 99.01 -- 0.21574 0.21316 0.26498 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 2.601 2.669 7128 395 7128 0.375 0.434 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.082
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] -0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.26
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.564
r_chiral_restr 0.112
r_mcbond_it 0.654
r_xyhbond_nbd_refined 0.172
r_gen_planes_refined 0.005
r_symmetry_hbond_refined 0.197
r_scbond_it 2.105
r_nbd_refined 0.234
r_dihedral_angle_1_deg 6.051
r_symmetry_vdw_refined 0.262
r_bond_refined_d 0.015
r_mcangle_it 1.279
r_scangle_it 3.533
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13260
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 546

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.25
HKL-2000 data reduction
SCALEPACK data scaling
SHARP phasing