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 (RAXIS HTC) RIGAKU 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_scangle_it 2.995
r_scbond_it 1.791
r_mcangle_it 1.236
r_mcbond_it 0.729
r_nbd_refined 0.221
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.091
r_dihedral_angle_4_deg 20.114
r_dihedral_angle_3_deg 15.567
r_dihedral_angle_2_deg 34.736
r_dihedral_angle_1_deg 6.188
r_angle_other_deg 0.858
r_angle_refined_deg 1.974
r_bond_other_d 0.001
r_bond_refined_d 0.017
r_nbd_other 0.186
r_nbtor_refined 0.189
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.15
r_symmetry_vdw_refined 0.117
r_symmetry_vdw_other 0.276
r_symmetry_hbond_refined 0.114
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

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
PHASER model building