X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 11 % Ethylene glycol, soaked in 0.5 M Na phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.23 α = 90
b = 138.97 β = 90
c = 141.82 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Osmic Mirrors 2007-10-04
Diffraction Radiation
Monochromator Protocol
Osmic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER 1.54179 -- --

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
1.85 50 99.3 -- 0.046 -- 3.5 49649 49649 0.0 0.0 23.9
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)
1.85 1.95 99.2 -- 0.542 1.9 3.1 --

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 1.85 20.0 -- 0.0 47049 47049 2517 98.75 -- 0.16784 0.16606 0.20265 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 1.85 1.899 -- 180 3157 0.341 0.373 -- 93.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.136
Anisotropic B[1][1] 0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.38
r_mcangle_it 0.889
r_nbd_refined 0.194
r_dihedral_angle_2_deg 34.687
r_symmetry_hbond_refined 0.143
r_mcbond_it 0.559
r_gen_planes_refined 0.004
r_angle_refined_deg 1.193
r_dihedral_angle_4_deg 16.947
r_scangle_it 2.555
r_dihedral_angle_3_deg 13.323
r_scbond_it 1.604
r_xyhbond_nbd_refined 0.147
r_chiral_restr 0.076
r_bond_refined_d 0.01
r_nbtor_refined 0.293
r_symmetry_vdw_refined 0.202
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.115
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3461
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 508

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MAR345dtb data collection
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing