X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3.7
Temperature 277.0
Details 43.1000% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.34 α = 90
b = 109.89 β = 104.84
c = 60.63 γ = 90
Symmetry
Space Group C 1 2 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) 2008-11-14
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 0.91162,0.97831,0.97870 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
1.35 29.99 98.2 0.082 0.082 -- 3.7 -- 99649 -- -- 14.166
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)
1.35 1.39 81.9 0.496 0.496 1.5 3.0 6124

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 1.35 29.988 -- 0.0 -- 99648 4983 98.22 -- 0.135 0.134 0.157 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 1.35 1.385 -- 283 5838 0.258 0.259 -- 81.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.461
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.96
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.29
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.223
r_mcangle_it 2.61
r_dihedral_angle_1_deg 5.547
r_mcbond_other 1.026
r_sphericity_bonded 3.701
r_xyhbond_nbd_refined 0.15
r_nbd_other 0.201
r_symmetry_hbond_refined 0.205
r_scangle_it 2.876
r_rigid_bond_restr 1.335
r_sphericity_free 7.409
r_gen_planes_other 0.002
r_bond_other_d 0.002
r_dihedral_angle_3_deg 12.78
r_dihedral_angle_4_deg 13.771
r_chiral_restr 0.086
r_mcbond_it 1.932
r_angle_refined_deg 1.504
r_symmetry_vdw_other 0.225
r_bond_refined_d 0.015
r_nbtor_other 0.089
r_symmetry_vdw_refined 0.267
r_nbtor_refined 0.185
r_dihedral_angle_2_deg 35.42
r_gen_planes_refined 0.008
r_scbond_it 2.093
r_angle_other_deg 0.941
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3077
Nucleic Acid Atoms 0
Heterogen Atoms 98
Solvent Atoms 347

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction