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 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 98.3 0.035 -- -- 4.7 -- 146753 -- -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 94.4 0.199 -- 4.5 3.2 --

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 -- -- -- 29323 1559 98.2 -- 0.137 0.136 0.157 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 -- 107 2052 0.238 0.229 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.61
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_scangle_it 4.084
r_scbond_it 2.816
r_mcangle_it 2.21
r_mcbond_it 1.46
r_nbd_refined 0.432
r_gen_planes_other 0.036
r_gen_planes_refined 0.009
r_chiral_restr 0.113
r_dihedral_angle_1_deg 5.586
r_angle_other_deg 4.017
r_angle_refined_deg 1.979
r_bond_other_d 0.0
r_bond_refined_d 0.02
r_nbd_other 0.292
r_nbtor_other 0.198
r_xyhbond_nbd_refined 0.219
r_symmetry_vdw_refined 0.222
r_symmetry_vdw_other 0.285
r_symmetry_hbond_refined 0.266
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SHARP model building