X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details ammonium phosphate, Tris-HCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.83 α = 90
b = 123.83 β = 90
c = 125.46 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors --
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.00 EMBL/DESY, Hamburg X12

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
1.44 43.7 99.8 0.0944 0.0944 -- 6.97 88705 88498 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)
1.44 1.54 98.8 0.6994 0.6994 2.13 6.08 --

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 1.44 39.62 -- -- 88498 82345 4358 99.24 -- 0.15899 0.15688 0.1995 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 1.441 1.479 -- 289 5438 0.342 0.368 -- 89.84
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 28.394
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 3.223
r_dihedral_angle_3_deg 14.979
r_angle_refined_deg 2.38
r_mcangle_it 4.386
r_dihedral_angle_2_deg 35.215
r_dihedral_angle_4_deg 16.415
r_mcbond_it 2.867
r_chiral_restr 0.195
r_bond_refined_d 0.034
r_dihedral_angle_1_deg 6.95
r_scbond_it 6.281
r_gen_planes_refined 0.012
r_scangle_it 9.187
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2625
Nucleic Acid Atoms 0
Heterogen Atoms 113
Solvent Atoms 394

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
DENZO data reduction
SCALEPACK data scaling