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_chiral_restr 0.114
r_gen_planes_refined 0.006
r_angle_refined_deg 1.457
r_dihedral_angle_2_deg 26.35
r_mcangle_it 1.554
r_scbond_it 1.161
r_dihedral_angle_3_deg 9.931
r_symmetry_vdw_refined 0.306
r_nbd_refined 0.242
r_scangle_it 1.574
r_dihedral_angle_4_deg 11.973
r_xyhbond_nbd_refined 0.208
r_mcbond_it 1.034
r_nbtor_refined 0.321
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 2.542
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

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