5M2K | pdb_00005m2k

Crystal structure of vancomycin-Zn(II) complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.2 M magnesium formate salt, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3	58.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.899	α = 90
b = 35.899	β = 90
c = 55.553	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	1	27.13	96.3	0.06	27	8.1		14362

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	1	1.05	81.9		0.137	13.7	4.3

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	1	27.13	12922	1440	99.53	0.0976	0.0968	0.1705	0.1045	0.1764	RANDOM	8.152

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	54.08
r_sphericity_free	28.441
r_dihedral_angle_3_deg	20.305
r_dihedral_angle_1_deg	12.455
r_sphericity_bonded	7.306
r_rigid_bond_restr	6.43
r_angle_other_deg	5.195
r_angle_refined_deg	2.307
r_mcangle_it	0.561
r_mcbond_it	0.552
r_mcbond_other	0.545
r_chiral_restr	0.179
r_bond_refined_d	0.038
r_gen_planes_refined	0.038
r_bond_other_d	0.018
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	160
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing