X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 9
Temperature 273.0
Details 65% (+/-)-2-Methyl-2,4-Pentanediol, 0.1 M Bicine pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.48 α = 90
b = 61.48 β = 90
c = 113.15 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2003-06-23
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.019943, 0.979764, 0.979570 ALS 8.3.1

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
1.85 56.57 99.9 -- 0.079 -- 6.7 19259 19259 -- -- 32.69
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)
1.85 1.9 100.0 -- 0.548 2.8 6.1 1385

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 1.85 41.63 -- -- -- 18226 975 99.85 -- 0.17301 0.17102 0.21199 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 1.85 1.898 -- 66 1316 0.227 0.247 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 18.923
Anisotropic B[1][1] 1.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.35
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 8.655
r_scbond_it 6.09
r_mcangle_it 3.349
r_mcbond_it 1.924
r_symmetry_hbond_refined 0.218
r_symmetry_vdw_other 0.406
r_symmetry_vdw_refined 0.151
r_bond_refined_d 0.019
r_bond_other_d 0.002
r_angle_refined_deg 1.55
r_angle_other_deg 0.815
r_dihedral_angle_1_deg 5.49
r_chiral_restr 0.081
r_gen_planes_refined 0.006
r_gen_planes_other 0.002
r_nbd_refined 0.193
r_nbd_other 0.245
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.211
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1322
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 150

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
RESOLVE model building
SOLVE model building
SCALA(CCP4 version: 4.2) data reduction
MOSFLM data collection