6JFO | pdb_00006jfo

Formyl-Met-Ala-Ser bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8.5	287	0.02M CaCl2, 0.1M MgCl2, 15% (v/v) Glycerol, 25% (w/v) PEG 4K, 0.05M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.24	61.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.733	α = 90
b = 120.831	β = 90
c = 47.393	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2018-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	50	99.1	0.085	0.088	0.025	10.5	9.3		35695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	95.5		0.481	0.523	0.197	0.457		5.2

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	1LM4	1.6	49.99	33910	1781	98.78	0.1838	0.182	0.1918	0.2187	0.2275	RANDOM	35.274

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.39
r_dihedral_angle_3_deg	12.971
r_dihedral_angle_4_deg	11.571
r_dihedral_angle_1_deg	6.411
r_angle_refined_deg	2.093
r_angle_other_deg	1.113
r_chiral_restr	0.156
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1468
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	23

Software

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