X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.92 α = 90
b = 65.92 β = 90
c = 40.58 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 85
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD BENT MIRROR 2002-03-30
Diffraction Radiation
Monochromator Protocol
SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393, 0.9796 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
1.2 30 98.1 0.033 -- -- 5.2 -- 159748 -- -3.0 --
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)
1.2 1.23 92.4 0.171 -- 5.5 3.5 --

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
MAD 1.2 40.0 -- -- -- 29290 1559 98.1 -- 0.125 0.124 0.147 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 1.2 1.23 -- 103 2026 0.146 0.162 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.96
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] -0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.019
r_symmetry_vdw_other 0.281
r_symmetry_hbond_refined 0.266
r_scbond_it 2.932
r_nbtor_other 0.176
r_angle_other_deg 1.66
r_gen_planes_other 0.014
r_xyhbond_nbd_refined 0.163
r_angle_refined_deg 1.83
r_mcbond_it 1.469
r_bond_other_d 0.003
r_nbd_refined 0.279
r_gen_planes_refined 0.01
r_scangle_it 4.288
r_dihedral_angle_1_deg 5.508
r_symmetry_vdw_refined 0.224
r_mcangle_it 2.234
r_chiral_restr 0.114
r_nbd_other 0.264
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 970
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 138

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
XDS data reduction
XSCALE data scaling
SHARP phasing