X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 282.0
Details 36-38% PEG8000, 100 mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.23 α = 90
b = 65.23 β = 90
c = 49.44 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.934000 ESRF ID14-2

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 58.5 99.6 0.063 0.063 -- 14.2 -- 10291 -- -- --
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 1.95 97.5 0.249 0.249 2.9 7.7 1446

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 1.85 28.25 -- 0.0 -- 10268 493 99.48 -- 0.157 0.154 0.197 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 -- 31 679 0.167 0.2 -- 93.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.734
Anisotropic B[1][1] 1.29
Anisotropic B[1][2] 0.65
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.94
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.025
r_dihedral_angle_1_deg 6.552
r_nbtor_other 0.094
r_dihedral_angle_3_deg 17.528
r_mcbond_it 3.132
r_scbond_it 4.986
r_mcbond_other 1.453
r_mcangle_it 3.764
r_bond_other_d 0.011
r_xyhbond_nbd_refined 0.338
r_nbtor_refined 0.182
r_dihedral_angle_2_deg 37.779
r_dihedral_angle_4_deg 19.843
r_symmetry_vdw_refined 0.099
r_symmetry_vdw_other 0.204
r_angle_other_deg 1.309
r_nbd_refined 0.249
r_angle_refined_deg 2.372
r_gen_planes_refined 0.01
r_nbd_other 0.265
r_rigid_bond_restr 3.342
r_gen_planes_other 0.01
r_sphericity_free 10.523
r_sphericity_bonded 7.483
r_symmetry_hbond_refined 0.265
r_chiral_restr 0.15
r_scangle_it 6.619
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 818
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 98

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000