9XWU | pdb_00009xwu

Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P06282-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	0.1M HEPES (pH 7.5), 0.2M sodium chloride, 25% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.352	α = 90
b = 80.047	β = 94.608
c = 138.599	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 9M		2025-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.00003	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.002	46.093	91.7	0.17	0.183	0.067	0.997	7.4	7.3		19212			24.85

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	2.002	2.178	88.4		1.169	0.446	0.66		7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.002	46.05	19212	1004	33.185	0.22	0.2185	0.2185	0.2528	0.2529	RANDOM	26.091

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]
0.131		-0.008	-0.123		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.571
r_dihedral_angle_6_deg	13.567
r_dihedral_angle_1_deg	6.896
r_lrange_it	6.781
r_dihedral_angle_2_deg	5.854
r_scangle_it	3.657
r_mcangle_it	2.992
r_scbond_it	2.123
r_angle_refined_deg	1.772
r_mcbond_it	1.696
r_nbtor_refined	0.279
r_symmetry_nbd_refined	0.179
r_nbd_refined	0.178
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.138
r_ncsr_local_group_1	0.077
r_symmetry_xyhbond_nbd_refined	0.059
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3570
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
MOLREP	phasing
Coot	model building
MxDC	data collection
PDB_EXTRACT	data extraction
STARANISO	data scaling