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_nbd_refined 0.213
r_gen_planes_refined 0.006
r_chiral_restr 0.12
r_dihedral_angle_1_deg 6.606
r_angle_refined_deg 1.672
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.141
r_symmetry_vdw_refined 0.211
r_symmetry_hbond_refined 0.192
r_mcbond_it 0.717
r_mcangle_it 1.403
r_scbond_it 2.331
r_scangle_it 3.568
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement