X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 6.5
Temperature 277.0
Details 0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.48 α = 117.34
b = 74.6 β = 100.95
c = 74.59 γ = 100.71
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APS sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2004-02-20
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM -- APS 19-BM

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 43.34 97.72 -- 0.106 -- 3.77 -- 54061 -- -- 30.41
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)
2.0 2.07 93.79 -- 0.522 2.58 3.43 5179

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 2.01 43.34 -- -- -- 51297 2755 97.23 -- 0.20575 0.20391 0.23995 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 2.01 2.058 -- 186 3357 0.314 0.377 -- 86.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.66
Anisotropic B[1][1] 1.11
Anisotropic B[1][2] 1.25
Anisotropic B[1][3] 1.4
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.75
Anisotropic B[3][3] 0.52
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.089
r_dihedral_angle_2_deg 39.602
r_nbd_other 0.199
r_symmetry_vdw_refined 0.136
r_gen_planes_refined 0.007
r_scbond_it 5.208
r_mcbond_other 0.4
r_nbd_refined 0.21
r_bond_other_d 0.002
r_dihedral_angle_1_deg 6.321
r_bond_refined_d 0.017
r_chiral_restr 0.096
r_scangle_it 7.09
r_angle_other_deg 0.964
r_dihedral_angle_4_deg 12.745
r_nbtor_refined 0.182
r_angle_refined_deg 1.615
r_dihedral_angle_3_deg 14.531
r_symmetry_hbond_refined 0.248
r_gen_planes_other 0.003
r_xyhbond_nbd_refined 0.176
r_symmetry_vdw_other 0.333
r_mcangle_it 2.875
r_mcbond_it 2.066
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5591
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 338

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0005