X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 303.0
Details ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.56 α = 90
b = 62.84 β = 100.86
c = 107.66 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 mirrors 2001-12-06
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.9 SPRING-8 BL45PX

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
1.3 99 85.0 0.034 -- -- -- 261943 146822 -- -- --
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)
1.3 1.34 58.6 0.297 -- 0.87 -- --

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
-- 1.4 12.0 -- -- 111789 111789 12385 90.11 0.168 0.168 0.16541 0.19187 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 1.4 1.436 -- 767 6717 0.239 0.272 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.799
Anisotropic B[1][1] 0.01
Anisotropic B[1][3] 0.3
Anisotropic B[2][2] 0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.933
r_nbtor_other 0.551
r_nbd_other 0.187
r_nbd_refined 0.238
r_gen_planes_other 0.002
r_gen_planes_refined 0.006
r_chiral_restr 0.092
r_dihedral_angle_2_deg 13.124
r_dihedral_angle_1_deg 3.587
r_angle_other_deg 1.347
r_angle_refined_deg 1.736
r_bond_other_d 0.001
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.189
r_xyhbond_nbd_other 0.136
r_symmetry_vdw_refined 0.152
r_symmetry_vdw_other 0.252
r_symmetry_hbond_refined 0.178
r_mcbond_it 1.006
r_mcangle_it 1.705
r_scbond_it 2.464
r_scangle_it 3.897
r_rigid_bond_restr 1.349
r_sphericity_free 2.594
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4968
Nucleic Acid Atoms 0
Heterogen Atoms 182
Solvent Atoms 655

Software

Computing
Computing Package Purpose
JUPITER210 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
Jupiter210 data collection