X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 293.0
Details PEG 10000, Imidazole/malate., pH 8.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.42 α = 118.55
b = 45.07 β = 92.63
c = 45.38 γ = 107.17
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2002-11-09
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.97887 ESRF ID14-4

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
1.6 25.91 84.4 0.057 0.057 -- 1.9 34113 31333 4.8 -- --
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)
1.6 1.69 84.4 0.122 0.122 4.8 1.5 --

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
MOLECULAR REPLACEMENT 1.6 20.0 4.8 -- 37118 29762 1565 84.4 0.176 0.17602 0.17433 0.20843 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 1.6 1.641 -- 82 1355 0.183 0.247 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.55
Anisotropic B[1][1] -0.34
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] -0.89
Anisotropic B[2][2] 0.47
Anisotropic B[2][3] 0.21
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.216
r_bond_other_d 0.004
r_angle_other_deg 2.853
r_symmetry_hbond_refined 0.193
r_dihedral_angle_1_deg 4.872
r_xyhbond_nbd_refined 0.161
r_mcbond_it 0.899
r_gen_planes_refined 0.009
r_angle_refined_deg 1.762
r_mcangle_it 1.635
r_bond_refined_d 0.015
r_gen_planes_other 0.016
r_symmetry_vdw_refined 0.132
r_scbond_it 2.564
r_nbd_other 0.248
r_scangle_it 3.945
r_chiral_restr 0.101
r_nbtor_other 0.101
r_symmetry_vdw_other 0.36
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1821
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 243

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement