27JY | pdb_000027jy

Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with Phthalate

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	7.4	293	0.1M sodium fluoride pH 7.4 20%PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.285	α = 90
b = 136.51	β = 90
c = 188.382	γ = 90

Symmetry
Space Group	C 2 2 21

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		2026-05-06	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	2.9	28.54	99.29	0.994	22.19	6.6		18141

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	2.9	3.004			0.931

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	AlphaFold	2.9	28.54	18136	906	99.354	0.194	0.192	0.192	0.2402	0.2408	53.193

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]
0.027			-0.239		0.212

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.519
r_dihedral_angle_6_deg	12.686
r_dihedral_angle_2_deg	9.386
r_dihedral_angle_1_deg	7.853
r_lrange_it	4.818
r_lrange_other	4.817
r_mcangle_it	2.607
r_mcangle_other	2.606
r_scangle_it	2.521
r_scangle_other	2.521
r_mcbond_it	1.511
r_mcbond_other	1.511
r_angle_refined_deg	1.499
r_scbond_it	1.436
r_scbond_other	1.436
r_angle_other_deg	0.533
r_symmetry_xyhbond_nbd_other	0.389
r_symmetry_xyhbond_nbd_refined	0.241
r_nbd_refined	0.229
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.177
r_nbd_other	0.169
r_symmetry_nbd_refined	0.159
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_2	0.068
r_ncsr_local_group_3	0.068
r_chiral_restr	0.067
r_ncsr_local_group_1	0.062
r_ncsr_local_group_4	0.062
r_ncsr_local_group_5	0.059
r_ncsr_local_group_6	0.055
r_bond_refined_d	0.006
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	6547
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	12

Software

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