X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 277.0
Details 1.0M Imidazole, pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.45 α = 90
b = 153.45 β = 90
c = 84.85 γ = 90
Symmetry
Space Group P 41 21 2

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 2008-03-16
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL MONOCHROMATOR MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97918 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
2.26 28.85 100.0 0.119 0.119 -- 7.6 -- 47944 -- -- 39.52
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)
2.26 2.32 100.0 0.871 0.871 0.9 7.7 --

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 2.26 28.855 -- -- -- 47880 2424 99.9 -- 0.198 0.196 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 2.26 2.32 -- 164 3316 0.247 0.287 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.33
Anisotropic B[1][1] 1.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.23
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.339
r_dihedral_angle_3_deg 11.809
r_mcbond_it 1.295
r_gen_planes_refined 0.006
r_nbd_other 0.149
r_symmetry_hbond_refined 0.118
r_symmetry_vdw_refined 0.129
r_angle_refined_deg 1.643
r_dihedral_angle_4_deg 14.722
r_xyhbond_nbd_refined 0.103
r_bond_other_d 0.004
r_chiral_restr 0.094
r_scbond_it 3.898
r_scangle_it 5.227
r_dihedral_angle_1_deg 3.945
r_nbtor_other 0.073
r_nbd_refined 0.181
r_nbtor_refined 0.154
r_mcangle_it 2.054
r_symmetry_vdw_other 0.278
r_bond_refined_d 0.015
r_dihedral_angle_2_deg 37.04
r_mcbond_other 0.317
r_gen_planes_other 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5198
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 244

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.2.0019
SCALA data scaling
PDB_EXTRACT data extraction version: 3.004
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing