X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Temperature 277.0
Details 34.0000% polyethylene glycol 400, 0.2000M lithium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.69 α = 90
b = 90.69 β = 90
c = 53.89 γ = 120
Symmetry
Space Group P 32

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) 2009-02-18
Diffraction Radiation
Monochromator Protocol
SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97908,0.97840 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
1.5 29.68 97.1 0.048 -- -- 3.77 -- 79258 -- -3.0 16.81
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)
1.5 1.55 95.2 0.552 -- 1.6 -- --

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 1.5 29.68 -- 0.0 -- 79234 3974 99.8 -- 0.145 0.143 0.167 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 1.5 1.54 -- 309 5515 0.219 0.235 -- 98.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.75
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.418
r_angle_refined_deg 1.584
r_dihedral_angle_2_deg 40.897
r_nbd_other 0.177
r_nbtor_other 0.088
r_scangle_it 5.051
r_angle_other_deg 1.134
r_chiral_restr 0.08
r_symmetry_vdw_refined 0.211
r_bond_other_d 0.004
r_mcbond_it 1.702
r_dihedral_angle_1_deg 5.308
r_symmetry_hbond_refined 0.164
r_dihedral_angle_4_deg 13.132
r_gen_planes_other 0.003
r_nbtor_refined 0.175
r_mcangle_it 2.354
r_scbond_it 3.678
r_xyhbond_nbd_refined 0.17
r_nbd_refined 0.2
r_metal_ion_refined 0.153
r_symmetry_vdw_other 0.24
r_dihedral_angle_3_deg 9.688
r_gen_planes_refined 0.007
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3342
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 553

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing