X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Details 20% PEG2K and 2mM MgCl2, pH 7.5, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.63 α = 90
b = 98.63 β = 90
c = 45.3 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-11-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA

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
2.24 98.53 89.0 0.052 -- -- 4.6 -- 21232 -- 0.0 --
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)
2.24 2.3 54.6 0.509 -- -- 4.3 --

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
-- 2.24 49.32 -- 0.0 -- 20008 1360 94.26 -- 0.2352 0.2313 0.2897 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 2.24 2.301 -- 108 1393 0.366 0.425 -- 96.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.9698
Anisotropic B[1][1] -3.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.71
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.494
r_xyhbond_nbd_refined 0.156
r_angle_other_deg 0.776
r_mcbond_it 2.431
r_gen_planes_refined 0.003
r_chiral_restr 0.074
r_nbd_other 0.181
r_symmetry_vdw_other 0.211
r_dihedral_angle_3_deg 17.251
r_metal_ion_refined 0.06
r_symmetry_hbond_refined 0.173
r_dihedral_angle_2_deg 32.284
r_dihedral_angle_1_deg 6.214
r_nbtor_refined 0.175
r_dihedral_angle_4_deg 15.285
r_gen_planes_other 0.001
r_nbtor_other 0.085
r_scangle_it 5.582
r_nbd_refined 0.195
r_scbond_it 4.185
r_bond_refined_d 0.01
r_bond_other_d 0.002
r_angle_refined_deg 1.278
r_symmetry_vdw_refined 0.144
r_mcangle_it 2.937
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2411
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 50

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.10
XDS data reduction
XSCALE data scaling