8BV9 | pdb_00008bv9

Acylphosphatase from E. coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.2 M AS 30% w/v PEG4K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.415	α = 90
b = 81.944	β = 90
c = 63.994	γ = 90

Symmetry
Space Group	C 2 2 2

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 4M		2021-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.55	41.97	99	0.094	0.109	0.053	0.998	10.2	6.5		3631			68.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.67			0.981	0.44	1.5

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	2.552	41.006	3630	162	98.534	0.208	0.2049	0.2142	0.2782	0.291	RANDOM	67.18

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]
-1.259			2.055		-0.796

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.205
r_lrange_other	15.196
r_dihedral_angle_3_deg	14.795
r_dihedral_angle_6_deg	12.575
r_scangle_it	11.988
r_scangle_other	11.71
r_mcangle_other	8.544
r_mcangle_it	8.538
r_dihedral_angle_2_deg	8.118
r_scbond_it	7.78
r_scbond_other	7.593
r_dihedral_angle_1_deg	7.316
r_mcbond_it	6.033
r_mcbond_other	5.988
r_angle_refined_deg	1.675
r_angle_other_deg	0.548
r_symmetry_xyhbond_nbd_refined	0.366
r_symmetry_nbd_other	0.195
r_nbd_refined	0.193
r_nbtor_refined	0.171
r_nbd_other	0.161
r_symmetry_nbd_refined	0.148
r_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_xyhbond_nbd_other	0.023
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	732
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing