X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.57
Temperature 277.0
Details NANODROP, 2.23M Ammonium sulfate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 173 α = 90
b = 173 β = 90
c = 192.57 γ = 120
Symmetry
Space Group P 64 2 2

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) 2007-05-04
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97904, 0.97932 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
2.5 29.96 99.9 0.126 0.126 -- 10.8 -- 59155 -- -- 50.53
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)
2.5 2.56 100.0 0.864 0.864 0.9 11.0 4302

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
MAD 2.5 29.961 -- 0.0 -- 59108 2988 99.91 -- 0.199 0.198 0.21 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 2.5 2.565 4300 183 4117 0.269 0.302 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.685
Anisotropic B[1][1] -0.36
Anisotropic B[1][2] -0.18
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.54
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.517
r_dihedral_angle_4_deg 9.125
r_dihedral_angle_3_deg 9.171
r_mcangle_it 2.556
r_nbtor_refined 0.173
r_nbtor_other 0.083
r_angle_other_deg 1.182
r_chiral_restr 0.067
r_angle_refined_deg 1.655
r_xyhbond_nbd_refined 0.16
r_dihedral_angle_2_deg 27.805
r_symmetry_vdw_refined 0.101
r_nbd_other 0.131
r_scbond_it 4.356
r_gen_planes_refined 0.006
r_bond_other_d 0.003
r_gen_planes_other 0.002
r_symmetry_hbond_refined 0.206
r_symmetry_vdw_other 0.092
r_scangle_it 6.54
r_dihedral_angle_1_deg 2.155
r_nbd_refined 0.178
r_mcbond_other 0.321
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5286
Nucleic Acid Atoms 0
Heterogen Atoms 113
Solvent Atoms 187

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
MolProbity model building version: 3beta29
SCALA data scaling
PDB_EXTRACT data extraction version: 3.00
MAR345 data collection version: CCD
MOSFLM data reduction
SOLVE phasing
RESOLVE phasing