26QV | pdb_000026qv

Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1M SODIUM MALONATE PH 7.0, 0.01M BARIUM CHLORIDE DI HYDRATE, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.612	α = 90
b = 245.492	β = 90
c = 191.658	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	RIGAKU HyPix-6000HE		2023-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3	27.38	99.72	0.947	11.23	11.23		83596

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.107			0.885

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	3	27.38	83568	4208	99.72	0.254	0.2514	0.2423	0.2944	0.2828	17.385

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]
2.734			6.467		-9.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.598
r_dihedral_angle_6_deg	13.756
r_dihedral_angle_2_deg	10.8
r_dihedral_angle_1_deg	6.556
r_lrange_it	3.895
r_lrange_other	3.895
r_mcangle_it	2.501
r_mcangle_other	2.501
r_scangle_it	2.431
r_scangle_other	2.431
r_mcbond_it	1.546
r_mcbond_other	1.546
r_scbond_it	1.479
r_scbond_other	1.479
r_angle_refined_deg	1.438
r_angle_other_deg	0.476
r_symmetry_xyhbond_nbd_refined	0.359
r_xyhbond_nbd_other	0.281
r_symmetry_nbd_refined	0.232
r_nbd_refined	0.224
r_nbd_other	0.224
r_symmetry_nbd_other	0.214
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.18
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21922
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing