X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Details 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.5 α = 90
b = 73.54 β = 90
c = 118.75 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.979 ESRF ID14-2

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
2.1 37.14 98.7 0.071 -- -- 6.0 16111 15633 0.0 0.0 37.7

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 2.1 34.86 -- 0.0 16111 15633 478 98.45 0.206 0.206 0.205 0.254 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 2.1 2.154 1012 31 981 0.283 0.277 -- 85.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.011
Anisotropic B[1][1] 0.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.47
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.478
r_dihedral_angle_2_deg 33.082
r_nbd_refined 0.212
r_symmetry_vdw_refined 0.17
r_mcbond_it 0.455
r_bond_refined_d 0.009
r_scbond_it 1.055
r_dihedral_angle_1_deg 9.342
r_dihedral_angle_3_deg 15.741
r_xyhbond_nbd_refined 0.299
r_mcangle_it 0.707
r_scangle_it 1.244
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.296
r_chiral_restr 0.163
r_nbtor_refined 0.309
r_dihedral_angle_4_deg 19.956
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1976
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 77

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
MOSFLM data reduction
SCALA data scaling
MOLREP phasing