X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.93
Temperature 293.0
Details 17.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.93, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.63 α = 90
b = 44.02 β = 96.17
c = 119.38 γ = 90
Symmetry
Space Group P 1 21 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) 2009-02-22
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 0.91837,0.97876,0.97828 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
1.95 29.42 96.9 0.039 -- -- 3.88 -- 41306 -- -3.0 31.69
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)
1.95 2.02 94.5 0.501 -- 1.7 -- --

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 1.95 29.424 -- 0.0 -- 41295 2079 99.2 -- 0.188 0.185 0.232 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 1.95 2.001 -- 149 2848 0.242 0.29 -- 98.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.863
Anisotropic B[1][1] 0.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.33
Anisotropic B[2][2] 0.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_symmetry_vdw_refined 0.231
r_mcbond_other 0.903
r_mcangle_it 2.966
r_dihedral_angle_3_deg 13.841
r_symmetry_hbond_refined 0.158
r_dihedral_angle_2_deg 37.978
r_dihedral_angle_4_deg 14.907
r_dihedral_angle_1_deg 4.703
r_angle_refined_deg 1.475
r_nbtor_other 0.085
r_nbd_other 0.179
r_nbtor_refined 0.185
r_gen_planes_refined 0.006
r_mcbond_it 2.005
r_nbd_refined 0.217
r_scbond_it 4.941
r_scangle_it 6.567
r_angle_other_deg 1.044
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_chiral_restr 0.089
r_xyhbond_nbd_refined 0.147
r_symmetry_vdw_other 0.296
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4424
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 254

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
autoSHARP phasing
SHELXD phasing