X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details NANODROP, 10.0% 2-propanol, 0.3M Calcium acetate, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.15 α = 100.72
b = 45.15 β = 103.86
c = 60.78 γ = 103.31
Symmetry
Space Group P 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) 2007-04-07
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97929 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
1.44 39.19 77.4 0.036 -- -- -- -- 40271 -- -- 25.909
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)
1.44 1.49 27.2 0.467 -- 2.2 -- 1355

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 1.44 39.193 -- 0.0 -- 40270 2034 78.61 0.17 0.17 0.168 0.199 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 1.44 1.478 1026 47 979 0.313 0.327 -- 27.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.534
Anisotropic B[1][1] -0.3
Anisotropic B[1][2] 0.56
Anisotropic B[1][3] -0.36
Anisotropic B[2][2] 1.94
Anisotropic B[2][3] -0.04
Anisotropic B[3][3] -1.57
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.234
r_bond_refined_d 0.017
r_scangle_it 6.738
r_angle_other_deg 0.96
r_nbd_refined 0.214
r_mcbond_it 1.966
r_scbond_it 4.781
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.124
r_dihedral_angle_2_deg 35.101
r_dihedral_angle_1_deg 4.871
r_angle_refined_deg 1.543
r_dihedral_angle_4_deg 16.797
r_symmetry_vdw_other 0.301
r_mcangle_it 2.694
r_nbtor_other 0.086
r_mcbond_other 0.529
r_chiral_restr 0.084
r_metal_ion_refined 0.107
r_nbd_other 0.205
r_dihedral_angle_3_deg 12.745
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.197
r_nbtor_refined 0.175
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2022
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 268

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
SHELX phasing
REFMAC refinement version: 5.2.0019
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
XDS data reduction
SHELXD phasing
autoSHARP phasing