X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 25% PEG3350 0.17M, (NH4)2SO4 15% GLYCEROL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.61 α = 90
b = 78.61 β = 90
c = 423.28 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRRORS 2005-10-23
Diffraction Radiation
Monochromator Protocol
SI111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA -- SLS X10SA

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
2.3 47 99.3 0.1 -- -- 14.9 -- 35817 -- 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)
2.3 2.39 93.9 0.59 -- 1.9 3.4 --

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 2.3 50.0 -- -- -- 33893 1778 99.3 -- 0.204 0.201 0.257 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 2.3 2.36 -- 114 2252 0.288 0.317 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.17
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.59
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 6.081
r_scangle_it 8.936
r_symmetry_vdw_other 0.232
r_mcangle_it 3.995
r_dihedral_angle_3_deg 17.836
r_symmetry_vdw_refined 0.166
r_symmetry_hbond_refined 0.149
r_nbd_refined 0.215
r_xyhbond_nbd_refined 0.168
r_gen_planes_refined 0.006
r_chiral_restr 0.088
r_scbond_it 7.76
r_angle_other_deg 1.017
r_nbd_other 0.191
r_dihedral_angle_4_deg 23.144
r_gen_planes_other 0.002
r_nbtor_refined 0.179
r_nbtor_other 0.092
r_mcbond_it 2.899
r_bond_other_d 0.002
r_angle_refined_deg 1.526
r_dihedral_angle_2_deg 39.336
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3989
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 149

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
XDS data reduction
XSCALE data scaling
PHASER phasing