3DAQ | pdb_00003daq

Crystal structure of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.9	281	16.7% PEG6000, NaF 135mM, LiCl 296mM, NaAC 100mM, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.41	α = 90.13
b = 67.573	β = 68.85
c = 77.998	γ = 72.29

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	ADSC QUANTUM 210		2008-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9536	Australian Synchrotron	MX1

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	1.45	30.25	91.4	0.057	0.057	18.8	3.9		190869	2	2	9.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	71.9		0.147	0.147	8.4	3.9	21900

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	1yxc	1.45	30.25	181258	9610	100	0.13371	0.13229	0.14	0.16084	0.17	RANDOM	8.073

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]
0.83	-0.08	-0.34	-0.38	-0.13	-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.069
r_dihedral_angle_3_deg	11.27
r_dihedral_angle_4_deg	11.077
r_dihedral_angle_1_deg	9.927
r_sphericity_free	2.812
r_scangle_it	2.63
r_scbond_it	1.762
r_sphericity_bonded	1.329
r_angle_refined_deg	1.271
r_mcangle_it	1.08
r_angle_other_deg	0.887
r_rigid_bond_restr	0.772
r_mcbond_it	0.767
r_symmetry_vdw_refined	0.255
r_mcbond_other	0.244
r_nbd_refined	0.216
r_symmetry_vdw_other	0.197
r_nbd_other	0.179
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.097
r_nbtor_other	0.087
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9024
Nucleic Acid Atoms
Solvent Atoms	1795
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing