X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 10.5
Temperature 277.0
Details NANODROP, 0.8M K2HPO4, 0.2M Li2SO4, 1.2M NaH2PO4, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.52 α = 90
b = 80.52 β = 90
c = 116.26 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-09
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97891 SSRL BL11-1

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 29.89 98.9 0.133 0.133 -- 7.4 -- 29640 -- -- --
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)
2.0 2.05 98.0 0.76 0.76 1.0 7.5 2136

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
SAD 2.0 29.894 -- 0.0 -- 29613 1504 98.51 0.194 0.194 0.192 0.236 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 2.0 2.052 2136 110 2026 0.231 0.275 -- 97.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.937
Anisotropic B[1][1] 2.41
Anisotropic B[1][2] 1.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.61
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 9.957
r_nbd_other 0.208
r_gen_planes_other 0.002
r_symmetry_vdw_refined 0.119
r_nbtor_other 0.088
r_scbond_it 5.093
r_chiral_restr 0.092
r_nbtor_refined 0.181
r_angle_other_deg 0.89
r_nbd_refined 0.201
r_symmetry_vdw_other 0.232
r_bond_refined_d 0.015
r_bond_other_d 0.002
r_mcbond_other 0.41
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.163
r_scangle_it 6.649
r_angle_refined_deg 1.501
r_dihedral_angle_3_deg 14.714
r_mcbond_it 2.066
r_dihedral_angle_1_deg 5.72
r_xyhbond_nbd_refined 0.155
r_dihedral_angle_2_deg 34.635
r_mcangle_it 2.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2029
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 297

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
SOLVE phasing
REFMAC refinement version: 5.2.0019
SCALA data scaling
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
MOSFLM data reduction
CCP4 data scaling version: (SCALA)