X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.6
Temperature 293.0
Details 17-22% PEG 1K 100mM TRIS 5mM UBP310, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.7 α = 90
b = 97.95 β = 90
c = 129.13 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2005-08-11
Diffraction Radiation
Monochromator Protocol
Double Crystal Si-220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-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
1.74 40 99.9 0.038 -- -- 4.9 64151 64151 1.0 1.0 25.16
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)
1.74 1.8 99.7 0.441 -- 3.38 4.9 --

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 1.74 33.41 -- 0.0 60378 60378 3218 99.92 0.18255 0.18255 0.18103 0.21135 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 1.74 1.785 -- 265 4373 0.21 0.252 -- 99.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.284
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.47
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.661
r_mcangle_it 1.718
r_dihedral_angle_3_deg 10.626
r_xyhbond_nbd_refined 0.228
r_dihedral_angle_4_deg 13.203
r_scangle_it 1.876
r_bond_refined_d 0.014
r_nbd_refined 0.262
r_symmetry_hbond_refined 0.227
r_nbtor_refined 0.32
r_dihedral_angle_1_deg 2.762
r_mcbond_it 1.123
r_scbond_it 1.33
r_dihedral_angle_2_deg 26.879
r_chiral_restr 0.124
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.276
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4014
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 482

Software

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