X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 0.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 143.92 α = 90
b = 143.92 β = 90
c = 50.19 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M MIRRORS 2012-03-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- Diamond I04-1

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
1.1 46.55 89.6 0.04 -- -- 9.1 -- 140945 -- 2.0 --
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)
1.1 1.16 49.5 0.21 -- 6.7 4.2 --

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 1.1 46.6 -- -- -- 133840 7105 89.53 -- 0.08362 0.08264 0.10208 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 1.1 1.129 -- 241 4702 0.117 0.129 -- 42.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.843
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.171
r_symmetry_hbond_refined 0.338
r_sphericity_free 36.735
r_gen_planes_refined 0.008
r_xyhbond_nbd_other 0.019
r_bond_refined_d 0.01
r_dihedral_angle_3_deg 12.157
r_nbtor_other 0.085
r_angle_refined_deg 1.394
r_rigid_bond_restr 1.588
r_dihedral_angle_1_deg 6.001
r_nbd_refined 0.275
r_sphericity_bonded 7.229
r_dihedral_angle_2_deg 33.099
r_nbd_other 0.172
r_chiral_restr 0.28
r_metal_ion_refined 0.054
r_angle_other_deg 0.816
r_symmetry_vdw_other 0.274
r_symmetry_vdw_refined 0.338
r_dihedral_angle_4_deg 16.668
r_gen_planes_other 0.001
r_nbtor_refined 0.188
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3429
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 724

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0025
XDS data reduction
SCALA data scaling
MOLREP phasing