X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.9
Temperature 293.0
Details 20% PEG 1K 100 mM Tris 5 mM UBP302, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.88 α = 90
b = 97.91 β = 90
c = 128.35 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
IMAGE PLATE MARRESEARCH Confocal mirrors 2005-08-28
Diffraction Radiation
Monochromator Protocol
Multilayer confocal mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-002 -- -- --

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
1.86 40 98.6 0.057 -- -- 7.1 52211 52211 1.0 1.0 28.08
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)
1.86 1.93 85.7 0.43 -- -- 6.4 --

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
FOURIER SYNTHESIS 1.87 38.92 -- 0.0 48777 48777 2595 99.8 0.19273 0.19273 0.19125 0.22036 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 1.866 1.915 -- 205 3476 0.275 0.344 -- 97.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.676
Anisotropic B[1][1] 0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.574
r_scbond_it 1.161
r_mcangle_it 1.554
r_mcbond_it 1.034
r_nbd_refined 0.242
r_gen_planes_refined 0.006
r_chiral_restr 0.114
r_dihedral_angle_4_deg 11.973
r_dihedral_angle_3_deg 9.931
r_dihedral_angle_2_deg 26.35
r_dihedral_angle_1_deg 2.542
r_angle_refined_deg 1.457
r_bond_refined_d 0.012
r_nbtor_refined 0.321
r_xyhbond_nbd_refined 0.208
r_symmetry_vdw_refined 0.306
r_symmetry_hbond_refined 0.288
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4014
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 416

Software

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