X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 1.6M ammonium sulfate, 100 mM sodium citrate, 5% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 208.6 α = 90
b = 208.6 β = 90
c = 136.36 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-08-23
Diffraction Radiation
Monochromator Protocol
SI(111) DOUBLE-CRYSTAL MONOCHROMATOR, BENT CYLINDRICAL SI-MIRROR (RH COATING) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9797 APS 14-BM-D

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 30 98.9 -- 0.082 -- 7.3 -- 51262 -- 0.0 50.36
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 2.59 90.3 -- 0.442 2.7 -- 4613

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 12.0 -- -- 46761 46761 1433 93.79 -- 0.18457 0.18318 0.23044 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 2.562 -- 98 2652 0.25 0.305 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.381
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.93
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.717
r_angle_refined_deg 1.672
r_bond_refined_d 0.016
r_symmetry_hbond_refined 0.192
r_dihedral_angle_1_deg 6.606
r_gen_planes_refined 0.006
r_xyhbond_nbd_refined 0.141
r_nbd_refined 0.213
r_scangle_it 3.568
r_chiral_restr 0.12
r_mcangle_it 1.403
r_symmetry_vdw_refined 0.211
r_scbond_it 2.331
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6602
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 348

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing