X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 100.0
Details Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.7 α = 90
b = 74.19 β = 90
c = 84.84 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 2003-02-08
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
1.6 25 99.1 0.074 -- -- 8.2 59165 58633 0.0 0.0 18.6
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)
1.6 1.66 98.3 0.491 -- 3.8 -- --

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 refinement followed by regular refinement 1.6 25.0 0.0 0.0 59514 56042 2945 99.15 0.1621 0.1568 0.15565 0.17901 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 1.6 1.686 7959 411 7959 0.189 0.212 0.212 14.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.863
Anisotropic B[1][1] -0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.94
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.442
r_scbond_it 2.078
r_mcangle_it 1.268
r_mcbond_it 0.692
r_symmetry_hbond_refined 0.14
r_symmetry_vdw_other 0.278
r_symmetry_vdw_refined 0.246
r_metal_ion_refined 0.09
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.387
r_angle_other_deg 0.998
r_dihedral_angle_1_deg 5.878
r_chiral_restr 0.085
r_gen_planes_refined 0.006
r_gen_planes_other 0.005
r_nbd_refined 0.214
r_nbd_other 0.244
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.162
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3436
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 464

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement