X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 273.0
Details 1.6M Magnesium Sulfate, 0.1M Bis-Tris, 8% PEG 400, 3% ethanol, 3mM L-Norvaline, 3mM Carbamoyl phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.15 α = 90
b = 99.15 β = 90
c = 463 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2006-07-13
Diffraction Radiation
Monochromator Protocol
Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1

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
2.2 49.57 73.8 0.082 -- -- 5.5 69827 51538 0.0 0.0 24.1
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)
2.2 2.28 43.9 0.307 -- 3.3 3.1 2981

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 2.2 49.568 0.0 0.0 51719 48946 2592 73.81 -- 0.17879 0.17561 0.23887 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 2.2 2.257 -- 115 2060 0.221 0.294 -- 43.15
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 19.994
Anisotropic B[1][1] -1.14
Anisotropic B[1][2] -0.57
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.72
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.208
r_angle_refined_deg 1.659
r_symmetry_hbond_refined 0.183
r_mcbond_it 0.883
r_scbond_it 2.503
r_dihedral_angle_3_deg 16.276
r_chiral_restr 0.117
r_mcangle_it 1.5
r_nbtor_refined 0.312
r_dihedral_angle_2_deg 33.212
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.174
r_dihedral_angle_1_deg 6.265
r_xyhbond_nbd_refined 0.196
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 18.548
r_scangle_it 4.03
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6978
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 572

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
Blu-Ice data collection
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing