X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.6
Temperature 293.0
Details PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.69 α = 90
b = 81.69 β = 90
c = 225.81 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2002-07-05
Diffraction Radiation
Monochromator Protocol
Pt-coated toroidal Si mirror for horizontal and vertical focusing followed by double flat Si crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.6037 NSLS X25

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
3.1 20 99.9 -- 0.07 -- 6.3 30657 30643 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)
3.1 3.21 99.6 -- 0.115 5.2 6.31 193476

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 + SAD 3.1 20.0 -- 0.0 15703 15679 837 99.85 -- 0.2259 0.2238 0.2646 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 3.1 3.175 -- 57 1089 0.236 0.389 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 23.448
Anisotropic B[1][1] -0.91
Anisotropic B[1][2] -0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.37
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.068
r_nbd_other 0.366
r_nbd_refined 0.391
r_gen_planes_other 0.018
r_gen_planes_refined 0.043
r_chiral_restr 0.409
r_dihedral_angle_3_deg 25.749
r_dihedral_angle_1_deg 12.159
r_angle_other_deg 1.259
r_angle_refined_deg 3.097
r_bond_other_d 0.001
r_bond_refined_d 0.032
r_xyhbond_nbd_refined 0.234
r_xyhbond_nbd_other 0.236
r_symmetry_vdw_refined 0.296
r_symmetry_vdw_other 0.332
r_symmetry_hbond_refined 0.275
r_mcbond_it 2.238
r_mcangle_it 3.632
r_scbond_it 5.949
r_scangle_it 8.661
Coordinate Error
Parameter Value
Luzzati Sigma A (R-Free Set) 0.464
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4630
Nucleic Acid Atoms 0
Heterogen Atoms 223
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SHARP model building
AMORE model building
SCALEPACK data reduction
HKL-2000 data collection