X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.64
Temperature 277.0
Details 32.0000% 2-methyl-2,4-pentanediol, 0.2000M magnesium chloride, 0.1M Imidazole pH 7.64, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.1 α = 90
b = 84.92 β = 90
c = 94.33 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 MAR MAR325 FLAT MIRROR (VERTICAL FOCUSING) 2009-02-19
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 0.91837,0.97889,0.97824 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
1.7 29.49 97.7 0.078 -- -- 4.05 -- 45480 -- -3.0 16.64
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)
1.7 1.76 93.0 0.614 -- 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
MAD 1.7 29.49 -- -- -- 45441 2293 98.8 -- 0.17 0.169 0.195 --
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 1.7 1.74 -- 177 3001 0.257 0.274 -- 95.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 7.85
Anisotropic B[1][1] 1.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_chiral_restr 0.077
r_scangle_it 2.498
r_dihedral_angle_3_deg 11.97
r_scbond_it 1.637
r_angle_other_deg 0.775
r_gen_planes_other 0.002
r_mcbond_it 0.532
r_mcangle_it 0.88
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 6.398
r_angle_refined_deg 1.279
r_dihedral_angle_4_deg 16.402
r_dihedral_angle_2_deg 35.843
r_mcbond_other 0.167
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3107
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 354

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
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