X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details 2.0M AS, 0.1M tris pH 8.5, 20mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.87 α = 90
b = 95.87 β = 90
c = 82.81 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 -- -- 2003-02-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM

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
2.18 50 92.2 0.056 -- 20.616 5.8 -- 21473 -- -- --
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)
2.18 2.26 95.0 0.444 -- -- 5.7 2169

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
-- 2.18 50.0 -- -- -- 21473 1114 92.2 -- 0.183 0.182 0.207 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 2.181 2.238 -- 86 1494 0.189 0.22 -- 94.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.08
Anisotropic B[1][1] -0.93
Anisotropic B[1][2] -0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.39
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.463
r_scbond_it 2.939
r_mcangle_it 1.788
r_mcbond_it 1.12
r_nbd_refined 0.216
r_gen_planes_refined 0.008
r_chiral_restr 0.137
r_dihedral_angle_4_deg 16.298
r_dihedral_angle_3_deg 17.481
r_dihedral_angle_2_deg 36.402
r_dihedral_angle_1_deg 6.418
r_angle_refined_deg 1.829
r_bond_refined_d 0.019
r_nbtor_refined 0.314
r_xyhbond_nbd_refined 0.153
r_symmetry_vdw_refined 0.229
r_symmetry_hbond_refined 0.158
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1927
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 125

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 refinement
HKL data processing