X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 296.0
Details 2M ammonium sulfate, 100 mM HEPES pH 7.5, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.2 α = 90
b = 160.2 β = 90
c = 133.48 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Double crystal Si(111) 2002-06-15
Diffraction Radiation
Monochromator Protocol
Double crystal Si(111) MAD
Double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 0.95666, 0.97926, 0.97955 ALS 5.0.2
SYNCHROTRON ALS BEAMLINE 5.0.2 1.1 ALS 5.0.2

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
2.7 50 98.1 0.047 -- -- 4.1 53383 52352 -- -- --
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)
2.7 2.8 84.1 0.481 -- 1.6 3.01 4467

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 2.7 20.0 -- 2.0 52185 49551 2634 98.05 0.24079 0.23872 0.23898 0.27442 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 2.701 2.77 -- 155 3013 0.346 0.344 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.46
Anisotropic B[1][1] 2.13
Anisotropic B[1][2] 1.07
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.2
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 7.188
r_bond_refined_d 0.018
r_angle_refined_deg 2.36
r_dihedral_angle_1_deg 2.73
r_chiral_restr 0.127
r_gen_planes_refined 0.015
r_nbd_refined 0.3
r_xyhbond_nbd_refined 0.195
r_symmetry_vdw_refined 0.306
r_symmetry_hbond_refined 0.295
r_mcbond_it 1.337
r_mcangle_it 2.597
r_scbond_it 4.622
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9213
Nucleic Acid Atoms 0
Heterogen Atoms 150
Solvent Atoms 42

Software

Computing
Computing Package Purpose
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement