5T1Q | pdb_00005t1q

2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FI7	3FI7, 2LRJ
experimental model	PDB	2LRJ	3FI7, 2LRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	292	Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: PACT (B2), 0.1M MIB (pH 5.0), 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.57	α = 108.7
b = 66.838	β = 104.72
c = 102.737	γ = 90.25

Symmetry
Space Group	P 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)	2016-08-11	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)	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	2.15	30	98.4	0.132	0.132	29.5	11.7		82976		-3	31.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	97.4		0.818	0.877	3.8	11.9

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	3FI7, 2LRJ	2.15	29.53	78670	3806	98.3	0.17524	0.1732	0.18	0.2189	0.23	RANDOM	40.809

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]
-1.08	-0.14	-0.63	2.17	-0.15	-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.049
r_dihedral_angle_4_deg	12.512
r_dihedral_angle_3_deg	10.303
r_long_range_B_refined	4.777
r_long_range_B_other	4.691
r_dihedral_angle_1_deg	2.81
r_mcangle_it	2.245
r_mcangle_other	2.245
r_scangle_other	2.117
r_angle_refined_deg	1.306
r_mcbond_it	1.276
r_mcbond_other	1.274
r_scbond_it	1.224
r_scbond_other	1.224
r_angle_other_deg	0.86
r_chiral_restr	0.084
r_gen_planes_refined	0.022
r_gen_planes_other	0.017
r_bond_refined_d	0.008
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	11300
Nucleic Acid Atoms
Solvent Atoms	780
Heterogen Atoms	16

Software

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