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_scbond_it 3.597
r_mcangle_it 3.044
r_mcbond_it 1.815
r_nbd_refined 0.217
r_gen_planes_refined 0.005
r_chiral_restr 0.093
r_dihedral_angle_4_deg 19.025
r_dihedral_angle_3_deg 17.634
r_dihedral_angle_2_deg 37.259
r_dihedral_angle_1_deg 5.466
r_angle_refined_deg 1.419
r_bond_refined_d 0.015
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.166
r_symmetry_vdw_refined 0.191
r_symmetry_hbond_refined 0.24
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.5_2) refinement
AMoRE model building