6MUQ | pdb_00006muq

1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 7.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PEG's II (D1), 0.1M Sodium acetate, 0.1M HEPES (pH 7.5), 22% (w/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.201	α = 90
b = 37.858	β = 115.75
c = 59.577	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD	C(111)	2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.67	30	99.9	0.072	0.072	0.083	0.039	22.4	4.3		26136		-3	27.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.7	99.9		0.709	0.709	0.814	0.395	0.766	2	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	6AZI	1.67	29.83	24714	1283	99.83	0.17091	0.16922	0.18	0.20354	0.22	RANDOM	35.818

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]
0.86		-2.31	0.06		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.024
r_dihedral_angle_4_deg	13.583
r_dihedral_angle_3_deg	9.521
r_long_range_B_refined	5.536
r_long_range_B_other	5.471
r_dihedral_angle_1_deg	3.001
r_scangle_other	2.727
r_mcangle_it	1.94
r_mcangle_other	1.94
r_scbond_it	1.719
r_scbond_other	1.717
r_angle_refined_deg	1.445
r_mcbond_it	1.271
r_mcbond_other	1.265
r_angle_other_deg	0.409
r_chiral_restr	0.062
r_gen_planes_refined	0.051
r_gen_planes_other	0.047
r_bond_refined_d	0.006
r_bond_other_d	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	2062
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing