X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 0.1 M Hepes pH 7.5, 12% MPD, and 4% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.02 α = 90
b = 90.02 β = 90
c = 183.14 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 121
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-04-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B -- APS 23-ID-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
2.8 50 99.8 0.086 0.128 -- 8.5 -- 9708 1.0 1.0 --
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)
2.8 2.91 100.0 0.823 0.716 3.7 8.6 1063

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 2.8 19.85 -- -- -- 9157 465 99.97 -- 0.2234 0.22104 0.2682 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 2.8 2.872 -- 38 657 0.281 0.389 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.83
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.242
r_symmetry_vdw_refined 0.285
r_chiral_restr 0.138
r_scangle_it 3.658
r_mcbond_it 0.935
r_nbtor_refined 0.333
r_nbd_refined 0.312
r_dihedral_angle_4_deg 23.528
r_mcangle_it 1.572
r_symmetry_hbond_refined 0.168
r_bond_refined_d 0.02
r_gen_planes_refined 0.007
r_angle_refined_deg 2.245
r_dihedral_angle_3_deg 24.667
r_xyhbond_nbd_refined 0.247
r_dihedral_angle_1_deg 8.909
r_scbond_it 2.431
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1994
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 11

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling