8ABU

Crystal structure of NaLdpA mutant H97Q in complex with erythro-DGPD

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 500 MME, 10% PEG 20000, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M Imidazole/MES buffer pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.384	α = 90
b = 66.002	β = 108.675
c = 107.051	γ = 90

Symmetry
Space Group	C 1 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		2020-10-22	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	1.661	56.234	94	0.087	0.036	0.999	12.8	7		69923

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	1.661	1.804	55.1		1.144	0.467	0.653	1.6	6.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7XXX	1.661	56.234	69923	3285	79.105	0.169	0.167	0.2009	30.674

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]
0.197		0.14	-0.037		-0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.549
r_dihedral_angle_4_deg	15.836
r_dihedral_angle_3_deg	14.429
r_dihedral_angle_1_deg	7.385
r_lrange_it	6.265
r_lrange_other	6.035
r_scangle_it	3.918
r_scangle_other	3.917
r_mcangle_it	3.36
r_mcangle_other	3.36
r_scbond_it	2.509
r_scbond_other	2.509
r_mcbond_it	2.175
r_mcbond_other	2.175
r_angle_refined_deg	1.701
r_angle_other_deg	1.461
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_refined	0.214
r_nbd_other	0.208
r_symmetry_xyhbond_nbd_other	0.196
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.117
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_2	0.073
r_ncsr_local_group_3	0.07
r_ncsr_local_group_1	0.067
r_xyhbond_nbd_other	0.045
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5709
Nucleic Acid Atoms
Solvent Atoms	647
Heterogen Atoms	23

Software

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