X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 1.0000M K/Na Tartrate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.84 α = 90
b = 103.84 β = 90
c = 128.97 γ = 120
Symmetry
Space Group P 62 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 collimating mirror, toroid focusing mirror 2008-07-16
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97934,0.97892 SSRL BL9-2

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
1.9 29.2 99.5 0.107 0.107 -- 7.1 -- 32785 -- -- 22.755
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)
1.9 1.95 99.7 0.625 0.625 1.0 7.2 2391

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 1.9 29.198 -- 0.0 -- 32757 1663 99.31 -- 0.16 0.158 0.181 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 1.9 1.949 -- 129 2262 0.2 0.274 -- 99.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.295
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.279
r_gen_planes_other 0.002
r_symmetry_vdw_refined 0.155
r_mcangle_it 1.546
r_dihedral_angle_2_deg 32.508
r_chiral_restr 0.099
r_bond_other_d 0.004
r_symmetry_vdw_other 0.14
r_bond_refined_d 0.013
r_angle_refined_deg 1.617
r_nbtor_other 0.072
r_nbtor_refined 0.156
r_nbd_refined 0.181
r_scangle_it 4.608
r_symmetry_hbond_refined 0.127
r_nbd_other 0.146
r_dihedral_angle_4_deg 11.465
r_dihedral_angle_3_deg 10.441
r_angle_other_deg 1.402
r_dihedral_angle_1_deg 4.117
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.091
r_mcbond_it 1.063
r_mcbond_other 0.165
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2379
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 311

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling
PDB_EXTRACT data extraction version: 3.004
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing