3QY9 | pdb_00003qy9

The Crystal Structure of Dihydrodipicolinate reductase 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	1ARZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil sitting drop	4.5	298	2.0M Ammonium sulfate, 0.2M Sodium actetate , pH 4.5, Microbatch under oil sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.9	α = 90
b = 112.44	β = 90
c = 131.61	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 225 mm CCD	Mirror	2010-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	1.8	29.64	98	0.086	0.092	12.7	6.9		115798	2.9	2.9	24.6

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	1.8	1.9	93.4		0.559	0.607	2.9	6.1	97586

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1ARZ	1.8	28.5	2	115798	109818	5791	97.63	0.199	0.198	0.21	0.225	0.24	RANDOM	30.05

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]
1.31			-0.26		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.251
r_dihedral_angle_4_deg	14.81
r_dihedral_angle_3_deg	13.008
r_dihedral_angle_1_deg	5.509
r_scangle_it	2.076
r_scbond_it	1.257
r_angle_refined_deg	1.046
r_mcangle_it	0.738
r_mcbond_it	0.388
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7495
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	130

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling