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_scangle_it 1.876
r_scbond_it 1.33
r_mcangle_it 1.718
r_mcbond_it 1.123
r_nbd_refined 0.262
r_gen_planes_refined 0.007
r_chiral_restr 0.124
r_dihedral_angle_4_deg 13.203
r_dihedral_angle_3_deg 10.626
r_dihedral_angle_2_deg 26.879
r_dihedral_angle_1_deg 2.762
r_angle_refined_deg 1.661
r_bond_refined_d 0.014
r_nbtor_refined 0.32
r_xyhbond_nbd_refined 0.228
r_symmetry_vdw_refined 0.276
r_symmetry_hbond_refined 0.227
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement