8ABW | pdb_00008abw

Crystal structure of SpLdpA in complex with threo-DGPD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		NaLdpA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 6000, 0.2 M MgCl2, 0.1 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.983	α = 90
b = 69.983	β = 90
c = 85.892	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	PIXEL	DECTRIS EIGER2 XE 16M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.711	86.085	94.7	0.166	0.038	0.999	12.9	20.2		22162

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.711	1.85	55.8		2.398	0.549	0.623	1.5	19.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	NaLdpA	1.83	85.892	16207	706	73.682	0.178	0.176	0.18	0.2289	0.24	32.791

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]
0.227	0.113		0.227		-0.735

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.661
r_dihedral_angle_3_deg	15.838
r_dihedral_angle_4_deg	15.101
r_dihedral_angle_1_deg	7.48
r_lrange_it	5.478
r_lrange_other	5.446
r_scangle_it	2.805
r_scangle_other	2.804
r_mcangle_it	2.21
r_mcangle_other	2.21
r_scbond_it	2.121
r_scbond_other	2.12
r_angle_refined_deg	1.665
r_mcbond_it	1.365
r_angle_other_deg	1.355
r_mcbond_other	1.353
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.181
r_nbd_other	0.179
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1992
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing