X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 277.0
Details 0.2000M NH4H2PO3, 20.0000% PEG-3350, No Buffer pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.97 α = 90
b = 81.3 β = 90
c = 93.79 γ = 90
Symmetry
Space Group P 21 21 21

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 2008-12-08
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- 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
1.85 29.18 98.6 0.097 -- -- -- -- 35856 -- -3.0 17.089
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)
1.85 1.92 97.5 0.578 -- 1.5 -- --

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 1.85 29.185 -- 0.0 -- 35802 1791 99.61 -- 0.171 0.169 0.213 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 1.85 1.898 -- 126 2415 0.231 0.322 -- 98.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.398
Anisotropic B[1][1] -0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.73
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.175
r_scangle_it 7.131
r_angle_refined_deg 1.439
r_dihedral_angle_1_deg 6.862
r_scbond_it 5.015
r_bond_other_d 0.001
r_angle_other_deg 1.004
r_dihedral_angle_4_deg 12.261
r_symmetry_vdw_refined 0.298
r_chiral_restr 0.087
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.146
r_mcbond_other 0.577
r_dihedral_angle_3_deg 13.81
r_gen_planes_refined 0.006
r_nbd_other 0.197
r_dihedral_angle_2_deg 35.525
r_mcbond_it 2.134
r_mcangle_it 2.829
r_bond_refined_d 0.016
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.155
r_nbd_refined 0.207
r_symmetry_vdw_other 0.331
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3246
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 459

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