4EYS | pdb_00004eys

Crystal structure of MccF-like protein from Streptococcus pneumoniae in complex with AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E94

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.2 M Ca(oAc)2, 0.1 M imidazol, 10% Peg 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.998	α = 90
b = 97.998	β = 90
c = 79.805	γ = 120

Symmetry
Space Group	P 3 2 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	ADSC QUANTUM 315r	mirrors	2012-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	1.58	32	100	0.079		10.7	60681	60681	2		31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.61	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD/MR	THROUGHOUT	4e94	1.58	32.077	2	60679	57608	3071	99.65	0.18	0.17036	0.16887	0.18	0.19756	0.2046	RANDOM	21.413

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]
1.36	0.68		1.36		-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_3_deg	12.629
r_dihedral_angle_4_deg	12.37
r_dihedral_angle_1_deg	6.239
r_angle_other_deg	2.195
r_angle_refined_deg	1.996
r_chiral_restr	0.125
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2727
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing