X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 295.0
Details 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.93 α = 90
b = 39.93 β = 90
c = 69.49 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-03-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8028 EMBL/DESY, HAMBURG X13

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
1.38 30 97.0 -- 0.056 -- 5.5 13185 13185 -- -3.0 21.65
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)
1.38 1.44 88.1 -- 0.414 2.7 3.1 1398

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 1.39 20.0 -- 0.0 13120 13120 656 97.76 0.13397 0.13397 0.13207 0.17046 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 1.39 1.426 841 45 841 0.264 0.313 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC, AT LATE STAGES OF REFINEMENT ANISOTROPIC
Mean Isotropic B 15.044
Anisotropic B[1][1] 1.17
Anisotropic B[1][2] 0.58
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.75
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 5.126
r_nbtor_other 0.09
r_nbd_other 0.246
r_nbd_refined 0.19
r_gen_planes_other 0.002
r_gen_planes_refined 0.011
r_chiral_restr 0.114
r_dihedral_angle_1_deg 5.179
r_angle_other_deg 0.879
r_angle_refined_deg 1.842
r_bond_other_d 0.003
r_bond_refined_d 0.02
r_xyhbond_nbd_refined 0.129
r_symmetry_vdw_refined 0.212
r_symmetry_vdw_other 0.366
r_symmetry_hbond_refined 0.258
r_mcbond_it 2.991
r_mcangle_it 4.075
r_scbond_it 3.992
r_scangle_it 5.918
r_rigid_bond_restr 2.246
r_sphericity_free 7.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 456
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 57

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.27 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.27 refinement