X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.0
Details 1.8 M sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.15 α = 109.39
b = 30.51 β = 97.39
c = 41.1 γ = 97.09
Symmetry
Space Group P -1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2007-12-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.95373 APS 23-ID-B

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
0.95 50 88.2 0.057 -- -- 4.3 62285 62285 -- -- --
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)
0.95 0.98 50.9 -- -- 1.8 3.5 3600

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
AB INITIO PHASING 0.95 38.13 -- -- -- 59134 3130 87.92 -- 0.18878 0.188 0.20326 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 0.95 0.975 -- 111 2262 0.494 0.553 -- 45.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.564
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.12
Anisotropic B[1][3] -0.21
Anisotropic B[2][2] -0.53
Anisotropic B[2][3] 0.1
Anisotropic B[3][3] 0.35
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.232
r_dihedral_angle_3_deg 13.919
r_angle_refined_deg 1.646
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_scbond_it 3.483
r_dihedral_angle_4_deg 14.498
r_mcbond_it 1.632
r_dihedral_angle_1_deg 5.446
r_mcbond_other 0.449
r_scangle_it 5.161
r_angle_other_deg 0.872
r_chiral_restr 0.098
r_gen_planes_refined 0.007
r_bond_refined_d 0.011
r_dihedral_angle_2_deg 29.988
r_mcangle_it 2.561
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 566
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 90

Software

Software
Software Name Purpose
SHELXD phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling