X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 0.1 M MSPG, 30% PEG1K, 0.5% DMSO, SITTING DROP, VAPOR DIFFUSION, 277 K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.1 α = 90
b = 98.1 β = 90
c = 80.04 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC MULTILAYER MIRRORS 2004-12-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
2.55 42.48 99.0 0.13 -- -- 6.7 -- 14259 -- 2.5 --
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)
2.55 2.65 97.0 0.51 -- 2.7 4.1 --

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 2.55 24.5 -- -- -- 13501 714 98.9 -- 0.195 0.192 0.248 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 2.55 2.62 -- 48 956 0.311 0.341 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.66
Anisotropic B[1][1] 1.37
Anisotropic B[1][2] 0.69
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.06
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.189
r_symmetry_hbond_refined 0.114
r_symmetry_vdw_other 0.276
r_nbd_other 0.186
r_mcbond_it 0.729
r_dihedral_angle_2_deg 34.736
r_mcangle_it 1.236
r_dihedral_angle_4_deg 20.114
r_gen_planes_other 0.001
r_scangle_it 2.995
r_dihedral_angle_1_deg 6.188
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 15.567
r_scbond_it 1.791
r_angle_refined_deg 1.974
r_angle_other_deg 0.858
r_bond_refined_d 0.017
r_nbtor_other 0.088
r_symmetry_vdw_refined 0.117
r_bond_other_d 0.001
r_nbd_refined 0.221
r_xyhbond_nbd_refined 0.15
r_chiral_restr 0.091
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2264
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 48

Software

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