X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 294.0
Details CITRATE BUFFER, AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.98 α = 90
b = 29.62 β = 101.33
c = 40.33 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Double crystal focusing mirrors 2002-03-08
Diffraction Radiation
Monochromator Protocol
Si (III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9187 APS 19-ID

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
1.5 50 96.8 0.084 -- -- 3.1 15460 15460 -- -3.0 13.7
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)
1.5 1.55 85.7 0.286 -- 2.5 2.1 1368

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 1.504 19.28 -- 1.0 -- 15460 770 100.0 -- 0.15472 0.15297 0.18694 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 1.504 1.543 -- 37 849 0.19 0.218 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.754
Anisotropic B[1][1] 2.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.57
Anisotropic B[2][2] -0.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.97
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.948
r_sphericity_free 2.933
r_rigid_bond_restr 1.577
r_scangle_it 4.06
r_scbond_it 2.602
r_mcangle_it 2.224
r_mcbond_it 1.36
r_symmetry_hbond_refined 0.259
r_symmetry_vdw_other 0.267
r_symmetry_vdw_refined 0.191
r_xyhbond_nbd_refined 0.18
r_bond_refined_d 0.016
r_bond_other_d 0.001
r_angle_refined_deg 1.734
r_angle_other_deg 2.095
r_dihedral_angle_1_deg 4.945
r_dihedral_angle_3_deg 18.984
r_chiral_restr 0.119
r_gen_planes_refined 0.008
r_gen_planes_other 0.002
r_nbd_refined 0.26
r_nbd_other 0.223
r_nbtor_other 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 819
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 140

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection