X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details PEG4000, pH 4.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.29 α = 90
b = 72.16 β = 90
c = 129.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MSC Blue Confocal Optics 2002-04-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-D 1.5418 -- --

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
1.51 62.5 -- -- 0.06 -- -- 81971 73142 0.0 -3.0 --
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)
1.51 1.63 -- -- 0.147 3.0 -- --

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 1.51 62.5 -- 0.0 82108 69386 3689 89.18 -- 0.17174 0.17079 0.1897 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 1.511 1.55 -- 19 496 0.282 0.322 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.55
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_symmetry_hbond_refined 0.121
r_mcbond_it 0.613
r_nbd_other 0.234
r_angle_other_deg 0.903
r_gen_planes_refined 0.006
r_rigid_bond_restr 1.334
r_angle_refined_deg 1.382
r_mcangle_it 1.104
r_scbond_it 1.664
r_nbd_refined 0.22
r_xyhbond_nbd_refined 0.124
r_bond_refined_d 0.012
r_sphericity_bonded 3.069
r_symmetry_vdw_other 0.226
r_nbtor_other 0.112
r_symmetry_vdw_refined 0.185
r_scangle_it 2.587
r_sphericity_free 5.32
r_gen_planes_other 0.004
r_dihedral_angle_1_deg 5.837
r_chiral_restr 0.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3693
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 322

Software

Computing
Computing Package Purpose
PROTEUM (BRUKER) Data Reduction (intensity integration)
BRUKER PROTEUM Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
Bruker version: Proteum data reduction
epmr model building
REFMAC version: 5.1.24 refinement
Bruker version: Proteum data collection