8ABV | pdb_00008abv

Crystal structure of SpLdpA in complex with erythro-DGPD

X-RAY DIFFRACTION

---

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	30% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.281	α = 90
b = 71.281	β = 90
c = 86.922	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		2022-02-05	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	1.683	86.922	86.5	0.194	0.044	0.999	13.3	19.9		23171

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	1.683	1.782	58.7		2.506	0.587	0.599	1.4	19

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	1.683	86.922	23170	1147	78.441	0.149	0.148	0.16	0.1768	0.18	23.274

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]
0.046	0.023		0.046		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.54
r_dihedral_angle_3_deg	13.182
r_dihedral_angle_4_deg	11.4
r_dihedral_angle_1_deg	7.172
r_lrange_it	6.158
r_lrange_other	5.927
r_scangle_it	4.344
r_scangle_other	4.343
r_scbond_it	2.79
r_scbond_other	2.789
r_mcangle_it	2.502
r_mcangle_other	2.501
r_angle_refined_deg	1.879
r_mcbond_other	1.68
r_mcbond_it	1.679
r_angle_other_deg	1.489
r_nbd_refined	0.212
r_nbd_other	0.201
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.16
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2005
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	63

Software

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