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 = 62.43 α = 90
b = 76.36 β = 90
c = 119.2 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 -- 2006-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 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
1.9 32.14 99.0 0.071 -- -- 6.5 22583 21902 0.0 0.0 23.5
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)
1.9 2.0 94.0 0.399 -- 4.1 5.2 --

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 1.9 32.14 -- 0.0 22583 21902 681 98.85 0.206 0.206 0.205 0.243 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 1.9 1.949 1487 45 1442 0.236 0.339 -- 89.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.318
Anisotropic B[1][1] 0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.03
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 0.891
r_xyhbond_nbd_refined 0.303
r_mcangle_it 0.663
r_dihedral_angle_2_deg 33.885
r_symmetry_hbond_refined 0.136
r_nbtor_refined 0.307
r_angle_refined_deg 1.403
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 10.04
r_symmetry_vdw_refined 0.143
r_dihedral_angle_1_deg 11.502
r_scangle_it 1.227
r_gen_planes_refined 0.003
r_nbd_refined 0.198
r_dihedral_angle_3_deg 14.225
r_mcbond_it 0.424
r_chiral_restr 0.113
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2051
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 59

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