5E9R | pdb_00005e9r

X-ray structure of the complex between lysozyme and the compound fac, cis-[RuII(CO)3Cl2(N3-MBI), MBI=N-methyl-benzimidazole

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Hen egg white lysozyme was incubated for 2 h in the presence of Ru-MBI in 1:10 protein to metal compound ratio. The adduct was then crystallized by using the hanging drop vapour diffusion method. Drops of 1 microliter were prepared at room temperature mixing 0.5 microliter of adduct at concentration 15 mg/mL with an equal amount of a reservoir constituted by 1.1 M NaCl, 0.1 M acetate buffer, pH 4.0. Crystals of the adduct grow within 24-48 hours.

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.5	α = 90
b = 78.5	β = 90
c = 36.309	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+		2014-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	55.5	99.4	0.085	12.9	6.2		5740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29	100		0.436	5	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.25	55.5	5452	261	99.41	0.15626	0.15228	0.16	0.23734	0.24	RANDOM	34.896

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.92			-0.92		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.117
r_dihedral_angle_4_deg	24.33
r_dihedral_angle_3_deg	14.361
r_long_range_B_refined	7.259
r_long_range_B_other	7.131
r_dihedral_angle_1_deg	6.725
r_scangle_other	4.918
r_mcangle_other	3.138
r_mcangle_it	3.113
r_scbond_it	3.047
r_scbond_other	2.998
r_angle_refined_deg	2.781
r_mcbond_it	2.095
r_mcbond_other	2.049
r_angle_other_deg	0.864
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	14

Software

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