X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 291.0
Details 1.6M sodium potassium phosphate pH 5.6, 3% MPD, soaking 100mM 1-Naphthol, 20% methanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.09 α = 90
b = 57.8 β = 109.89
c = 60.69 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 DECTRIS PILATUS 6M KB mirrors 2015-12-17
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC

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
1.13 48.04 99.0 0.066 -- -- 5.9 -- 124527 -- -- --
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)
1.13 1.14 -- 0.605 -- 2.0 -- --

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
FOURIER SYNTHESIS 1.13 48.04 -- -- -- 118360 6134 98.97 -- 0.16642 0.16596 0.17536 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 1.125 1.154 -- 394 7931 0.24 0.247 -- 89.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.996
Anisotropic B[1][1] -0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.45
Anisotropic B[2][2] -0.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 0.723
r_chiral_restr 0.082
r_gen_planes_other 0.009
r_bond_other_d 0.004
r_angle_other_deg 0.961
r_scbond_other 0.723
r_mcangle_other 0.924
r_mcbond_other 0.516
r_bond_refined_d 0.006
r_sphericity_bonded 3.343
r_scangle_other 1.175
r_long_range_B_refined 3.985
r_dihedral_angle_3_deg 11.918
r_long_range_B_other 3.985
r_dihedral_angle_2_deg 32.44
r_mcangle_it 0.925
r_angle_refined_deg 1.351
r_dihedral_angle_1_deg 5.824
r_rigid_bond_restr 26.588
r_gen_planes_refined 0.007
r_dihedral_angle_4_deg 17.054
r_mcbond_it 0.515
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2510
Nucleic Acid Atoms 0
Heterogen Atoms 206
Solvent Atoms 438

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XDS data reduction version: 0.72
Aimless data scaling version: 0.5.32
MOLREP phasing version: 11.5.02