1V0T | pdb_00001v0t

Phospholipase D from Streptomyces sp. strain PMF soaked with the product glycerophosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F0I	PDB ENTRY 1F0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.4		0.2 M NH4AC, 0.1 M CITRATE/ PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE-FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40

Crystal Properties
Matthews coefficient	Solvent content
2	38.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.16	α = 90
b = 56.94	β = 93.48
c = 68.81	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	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.53	69.01	95.8	0.051	8.6	3.4		61938

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.61	90.9		0.239	3	3.3

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 (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	PDB ENTRY 1F0I	1.53	69.01	61938	1927	95.8	0.157	0.156	0.17	0.188	0.2	RANDOM	15.18

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]
-0.78		-0.31	0.4		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.773
r_scangle_it	3.465
r_scbond_it	2.229
r_angle_refined_deg	1.822
r_mcangle_it	1.579
r_angle_other_deg	0.919
r_mcbond_it	0.889
r_symmetry_vdw_other	0.256
r_nbd_other	0.252
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.128
r_symmetry_hbond_refined	0.113
r_symmetry_vdw_refined	0.112
r_chiral_restr	0.095
r_nbtor_other	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3694
Nucleic Acid Atoms
Solvent Atoms	583
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
CNS	phasing