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 (PILATUS 2M) DECTRIS 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_sphericity_bonded 7.229
r_sphericity_free 36.735
r_rigid_bond_restr 1.588
r_nbd_refined 0.275
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.28
r_dihedral_angle_4_deg 16.668
r_dihedral_angle_3_deg 12.157
r_dihedral_angle_2_deg 33.099
r_dihedral_angle_1_deg 6.001
r_angle_other_deg 0.816
r_angle_refined_deg 1.394
r_bond_other_d 0.001
r_bond_refined_d 0.01
r_nbd_other 0.172
r_nbtor_refined 0.188
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.171
r_xyhbond_nbd_other 0.019
r_metal_ion_refined 0.054
r_symmetry_vdw_refined 0.338
r_symmetry_vdw_other 0.274
r_symmetry_hbond_refined 0.338
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.7.0025 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0025 refinement
MOLREP model building