X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 295.0
Details 0.1M Sodium citrate pH 5.5, 23% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.72 α = 90
b = 119.39 β = 90
c = 63.67 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 78
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2006-03-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.97872 APS 5ID-B

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
2.4 79.79 94.2 0.117 0.108 -- 6.9 16304 16259 -- -- --
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)
2.4 2.53 95.7 0.689 0.637 2.2 6.9 --

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 2.4 79.56 -- -- -- 15419 821 99.61 -- 0.2025 0.20004 0.24772 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 2.4 2.462 -- 55 1136 0.243 0.311 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.261
Anisotropic B[1][1] 3.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.49
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.461
r_angle_refined_deg 1.419
r_xyhbond_nbd_refined 0.166
r_dihedral_angle_2_deg 37.259
r_bond_refined_d 0.015
r_symmetry_vdw_refined 0.191
r_chiral_restr 0.093
r_gen_planes_refined 0.005
r_nbd_refined 0.217
r_mcangle_it 3.044
r_dihedral_angle_4_deg 19.025
r_symmetry_hbond_refined 0.24
r_dihedral_angle_3_deg 17.634
r_nbtor_refined 0.311
r_dihedral_angle_1_deg 5.466
r_mcbond_it 1.815
r_scbond_it 3.597
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2203
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 29

Software

Software
Software Name Purpose
AMoRE phasing
PHENIX refinement version: (phenix.refine: 1.5_2)
XDS data reduction
SCALA data scaling
REFMAC refinement version: 5.2.0019