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_rigid_bond_restr 2.246
r_mcangle_it 4.075
r_nbtor_other 0.09
r_nbd_refined 0.19
r_scbond_it 3.992
r_mcbond_it 2.991
r_bond_refined_d 0.02
r_angle_other_deg 0.879
r_angle_refined_deg 1.842
r_nbd_other 0.246
r_sphericity_bonded 5.126
r_gen_planes_refined 0.011
r_scangle_it 5.918
r_xyhbond_nbd_refined 0.129
r_symmetry_hbond_refined 0.258
r_sphericity_free 7.14
r_symmetry_vdw_refined 0.212
r_dihedral_angle_1_deg 5.179
r_bond_other_d 0.003
r_symmetry_vdw_other 0.366
r_chiral_restr 0.114
r_gen_planes_other 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 515
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 60

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.27
XDS data reduction
XDS data scaling
AMoRE phasing