X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 291.0
Details 1.7 mM ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.22 α = 90
b = 90.22 β = 90
c = 148.04 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-10-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1

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
2.15 30 98.2 0.1 -- -- 3.1 -- 12580 -- -- --
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)
2.15 2.19 95.9 0.134 -- -- 1.9 --

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 2.15 15.0 -- -- -- 11888 610 97.89 -- 0.17369 0.17161 0.21401 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 2.15 2.209 -- 47 835 0.2 0.201 -- 95.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.401
Anisotropic B[1][1] 2.22
Anisotropic B[1][2] 1.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.33
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.967
r_scbond_it 2.808
r_mcangle_it 2.127
r_mcbond_other 0.21
r_mcbond_it 1.287
r_nbd_refined 0.19
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_chiral_restr 0.144
r_dihedral_angle_4_deg 16.44
r_dihedral_angle_3_deg 13.944
r_dihedral_angle_2_deg 35.564
r_dihedral_angle_1_deg 5.575
r_angle_refined_deg 2.114
r_bond_refined_d 0.024
r_nbd_other 0.207
r_nbtor_refined 0.199
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.232
r_symmetry_vdw_refined 0.215
r_symmetry_vdw_other 0.373
r_symmetry_hbond_refined 0.239
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 990
Nucleic Acid Atoms 405
Heterogen Atoms 40
Solvent Atoms 143

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0019 refinement
HKL data reduction