5OB8

X-ray structure of the adduct formed upon reaction of lysozyme with the compound fac-[RuII(CO)3Cl2(N3-MIM), MIM=methyl-imidazole (crystals grown using NaCl)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 1.1M NaCl, 0.1 M sodium acetate pH 4.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.57 α = 90
b = 78.57 β = 90
c = 36.66 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 mirrors 2014-04-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
1.85 55.56 92.3 0.048 -- -- 4.9 -- 9488 -- -- --
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)
1.85 1.88 -- 0.603 -- 2.3 -- --

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
MOLECULAR REPLACEMENT 1.85 55.56 -- -- -- 8981 457 92.08 -- 0.163 0.15955 0.2298 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 1.85 1.898 -- 31 577 0.256 0.366 -- 85.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.256
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.107
r_scangle_other 5.073
r_dihedral_angle_2_deg 37.271
r_bond_refined_d 0.027
r_scbond_other 3.445
r_angle_refined_deg 1.838
r_scbond_it 3.573
r_dihedral_angle_1_deg 7.06
r_mcangle_other 3.535
r_bond_other_d 0.002
r_mcbond_it 2.812
r_long_range_B_refined 6.774
r_chiral_restr 0.123
r_mcbond_other 2.765
r_dihedral_angle_3_deg 14.362
r_dihedral_angle_4_deg 20.179
r_gen_planes_refined 0.009
r_gen_planes_other 0.002
r_mcangle_it 3.537
r_long_range_B_other 6.776
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1000
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 136

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing