X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 30% PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES. (Crystals were soaked in mother liquor containing 0.5 M calcium chloride for 5 hours.) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.88 α = 90
b = 44.97 β = 110.72
c = 72.11 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-11-10
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 0.8700 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
1.3 50.31 90.3 0.08 -- -- 2.9 73179 73179 0.0 0.0 --
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)
1.3 1.334 77.1 0.45 -- 2.1 2.6 --

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 1.3 50.0 -- 0.0 73179 73179 3654 90.28 -- 0.13445 0.13261 0.1693 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 1.3 1.334 -- 227 4201 0.226 0.284 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model protein and ligands were treated anisotropically while the solvent was isotropic
Mean Isotropic B 12.132
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.27
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 5.36
r_sphericity_free 6.221
r_rigid_bond_restr 2.631
r_scangle_it 6.143
r_scbond_it 4.396
r_mcangle_it 3.214
r_mcbond_it 2.399
r_nbd_refined 0.269
r_gen_planes_other 0.003
r_gen_planes_refined 0.008
r_chiral_restr 0.113
r_dihedral_angle_3_deg 15.123
r_dihedral_angle_1_deg 6.181
r_angle_other_deg 1.253
r_angle_refined_deg 1.723
r_bond_other_d 0.0
r_bond_refined_d 0.016
r_nbd_other 0.225
r_nbtor_other 0.383
r_xyhbond_nbd_refined 0.267
r_xyhbond_nbd_other 0.296
r_metal_ion_refined 0.087
r_symmetry_vdw_refined 0.259
r_symmetry_vdw_other 0.274
r_symmetry_hbond_refined 0.254
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2718
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 446

Software

Computing
Computing Package Purpose
ADSC Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
REFMAC version: 5.0 model building
SCALA data reduction
ADSC version: collection software data collection