X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 290.0
Details Sodium acetate, NaCl, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.05 α = 90
b = 65.35 β = 90
c = 138.56 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 2000-11-09
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 0.870 SRS PX9.6

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
1.22 10 93.4 0.035 -- -- 8.3 141368 141368 0.0 -3.0 --
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)
1.22 1.24 63.3 0.219 -- 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
MIR 1.22 10.0 -- 0.0 141368 141368 7075 93.4 -- 0.12437 0.12284 0.15391 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 1.22 1.251 -- 352 6913 0.17 0.212 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 13.54
Anisotropic B[1][1] -0.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.35
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.152
r_nbtor_other 0.209
r_nbd_other 0.201
r_nbd_refined 0.381
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_chiral_restr 0.14
r_dihedral_angle_2_deg 17.231
r_dihedral_angle_1_deg 17.245
r_angle_other_deg 3.001
r_angle_refined_deg 1.749
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.309
r_xyhbond_nbd_other 0.286
r_symmetry_vdw_refined 0.367
r_symmetry_vdw_other 0.288
r_symmetry_hbond_refined 0.351
r_mcbond_it 3.812
r_mcangle_it 5.374
r_scbond_it 8.663
r_scangle_it 10.982
r_rigid_bond_restr 2.365
r_sphericity_free 24.095
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3314
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 935

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5, CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection