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 PEG3350, 25mM MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.71 α = 90
b = 84.47 β = 92.13
c = 121.34 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Bent Cylinder, 1:1 defocused rhodium-coated electroless nickel-plated bent aluminum cylinder 2001-10-12
Diffraction Radiation
Monochromator Protocol
Double flat crystal fixed-exit monochromator using Si(111) flats SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 1.01715 NSLS X12B

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 30 99.9 -- 0.074 -- 7.5 122580 121366 0.0 0.0 --
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 2.05 99.9 0.578 -- 3.5 -- --

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 2.0 30.0 0.0 0.0 122580 121366 6421 99.99 0.23 0.22058 0.21887 0.25293 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 2.0 2.052 -- 480 8863 0.244 0.294 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.229
Anisotropic B[1][1] 1.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.98
Anisotropic B[2][2] 0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.69
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.188
r_sphericity_free 3.612
r_bond_refined_d 0.012
r_symmetry_hbond_refined 0.371
r_rigid_bond_restr 0.902
r_nbtor_other 0.065
r_mcangle_it 1.067
r_nbd_refined 0.284
r_scbond_it 1.507
r_angle_other_deg 0.811
r_chiral_restr 0.09
r_xyhbond_nbd_other 0.357
r_nbd_other 0.229
r_gen_planes_other 0.049
r_bond_other_d 0.007
r_angle_refined_deg 1.435
r_symmetry_vdw_other 0.328
r_scangle_it 2.228
r_symmetry_vdw_refined 0.334
r_mcbond_it 0.658
r_dihedral_angle_2_deg 16.406
r_dihedral_angle_1_deg 4.288
r_symmetry_hbond_other 0.532
r_gen_planes_refined 0.008
r_sphericity_bonded 1.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13136
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 416

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.0
HKL-2000 data reduction