X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Technique Under Oil
pH 8.5
Temperature 277.0
Details 20% v/v polyethylene glycol 300, 100 mM TRIS-HCl (pH 8.5), 5% w/v polyethylene glycol 8000, 10% v/v anhydrous glycerol, microbatch technique under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.06 α = 90
b = 79.91 β = 90
c = 186.44 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 130 mm Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror --
Diffraction Radiation
Monochromator Protocol
Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.9797 NSLS X4C

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
1.68 30 94.8 0.08 -- -- 4.3 -- 91701 -- -- --
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)
1.68 1.74 95.4 0.38 -- 2.03 3.2 9098

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
-- 1.68 25.0 -- 0.0 -- 91277 4529 94.82 -- 0.202 0.2 0.239 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 1.68 1.723 6303 339 6303 0.273 0.326 -- 95.23
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.169
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.62
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.014
r_symmetry_vdw_refined 0.207
r_angle_refined_deg 1.494
r_gen_planes_refined 0.007
r_dihedral_angle_1_deg 5.757
r_dihedral_angle_2_deg 26.203
r_scangle_it 3.459
r_nbd_refined 0.207
r_chiral_restr 0.098
r_scbond_it 2.136
r_mcbond_it 0.792
r_nbtor_refined 0.307
r_symmetry_hbond_refined 0.137
r_dihedral_angle_3_deg 14.178
r_mcangle_it 1.14
r_dihedral_angle_4_deg 16.83
r_xyhbond_nbd_refined 0.129
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6203
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 708

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling