X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 20mM MGAC2, 13% MPD, 100mM MES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.04 α = 90
b = 300.38 β = 112.97
c = 146.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-10-26
Diffraction Radiation
Monochromator Protocol
LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA

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
2.9 20 95.4 0.085 -- -- 2.6 238743 227749 2.0 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)
2.9 3.0 97.4 0.451 -- 1.9 -- --

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 2.9 15.0 2.0 -- 227749 216361 11388 95.51 0.189 0.18511 0.18385 0.20947 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 2.9 2.972 -- 829 15746 0.315 0.358 -- 97.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.807
Anisotropic B[1][1] 5.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.88
Anisotropic B[2][2] -11.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.95
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.778
r_gen_planes_other 0.001
r_bond_other_d 0.002
r_dihedral_angle_3_deg 19.528
r_scbond_other 3.189
r_dihedral_angle_1_deg 6.462
r_mcangle_it 3.788
r_mcbond_it 3.114
r_sphericity_bonded 7.564
r_chiral_restr 0.063
r_mcangle_other 3.788
r_sphericity_free 31.464
r_dihedral_angle_4_deg 17.552
r_gen_planes_refined 0.003
r_long_range_B_refined 4.181
r_scangle_other 3.504
r_angle_refined_deg 1.121
r_rigid_bond_restr 1.793
r_dihedral_angle_2_deg 37.089
r_mcbond_other 3.114
r_bond_refined_d 0.005
r_scbond_it 3.189
r_long_range_B_other 4.168
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49295
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 211

Software

Software
Software Name Purpose
XDS data scaling
REFMAC refinement
XDS data reduction
XSCALE data scaling
REFMAC phasing