X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details PEGII from Nextal condition G11, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.8 α = 90
b = 60.7 β = 103.36
c = 78.86 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal 2008-10-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97 SOLEIL PROXIMA 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
2.5 20 97.4 -- 0.104 -- 4.0 23764 23129 2.0 2.0 44.0
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)
2.5 2.64 94.9 -- 0.509 4.2 4.0 3583

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 2.5 19.86 -- -- -- 21958 1156 100.0 -- 0.22549 0.22212 0.28994 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 2.5 2.564 -- 85 1601 0.288 0.35 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.173
r_angle_refined_deg 1.091
r_dihedral_angle_4_deg 19.589
r_angle_other_deg 0.81
r_symmetry_vdw_refined 0.154
r_dihedral_angle_1_deg 5.95
r_nbd_refined 0.201
r_xyhbond_nbd_other 0.024
r_dihedral_angle_3_deg 18.197
r_gen_planes_refined 0.003
r_symmetry_vdw_other 0.235
r_bond_refined_d 0.008
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 37.158
r_nbtor_other 0.085
r_nbd_other 0.182
r_nbtor_refined 0.179
r_bond_other_d 0.001
r_xyhbond_nbd_refined 0.132
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4769
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 123

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
REFMAC refinement version: 5.2.0019
XDS data reduction
XDS data scaling