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 Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.65 α = 90
b = 74.19 β = 90
c = 85.4 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2002-11-07
Diffraction Radiation
Monochromator Protocol
Bent Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C

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
1.9 25 97.3 0.6 -- -- 3.5 36023 35051 0.0 0.0 21.9
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)
1.9 1.97 97.8 0.358 -- 3.4 -- --

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
rigid body followed by regular refinement 1.9 24.85 0.0 0.0 35014 33259 1753 97.24 0.16858 0.1669 0.1669 0.20113 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 1.9 2.002 4766 258 4766 0.213 0.26 -- 14.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.36
Anisotropic B[1][1] -1.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.09
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.735
r_nbd_other 0.241
r_symmetry_vdw_refined 0.19
r_mcangle_it 1.106
r_bond_other_d 0.002
r_scangle_it 2.875
r_nbd_refined 0.198
r_chiral_restr 0.083
r_nbtor_other 0.083
r_angle_other_deg 0.832
r_xyhbond_nbd_refined 0.16
r_symmetry_vdw_other 0.3
r_gen_planes_refined 0.005
r_symmetry_hbond_refined 0.199
r_angle_refined_deg 1.266
r_dihedral_angle_1_deg 5.729
r_bond_refined_d 0.01
r_gen_planes_other 0.004
r_mcbond_it 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3418
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 341

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
SCALEPACK data scaling
CNS phasing