26ZA | pdb_000026za

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

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 pH7.0 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.708	α = 90
b = 137.45	β = 90
c = 190.309	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		2026-01-27	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	2.8	28.542	99.61	0.994	38.3	20.9		20682

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	2.8	2.9			0.977

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	2.8	28.542	20658	1044	99.643	0.244	0.2423	0.2402	0.2836	0.2819	53.426

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]
-1.611			-4.274		5.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.275
r_dihedral_angle_6_deg	12.875
r_dihedral_angle_2_deg	8.24
r_dihedral_angle_1_deg	8.113
r_lrange_it	4.429
r_lrange_other	4.428
r_mcangle_it	2.762
r_mcangle_other	2.762
r_scangle_it	2.344
r_scangle_other	2.344
r_angle_refined_deg	1.715
r_mcbond_it	1.599
r_mcbond_other	1.599
r_scbond_it	1.335
r_scbond_other	1.335
r_angle_other_deg	0.635
r_symmetry_xyhbond_nbd_refined	0.276
r_nbd_refined	0.232
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.187
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.136
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_3	0.079
r_ncsr_local_group_5	0.079
r_ncsr_local_group_6	0.073
r_ncsr_local_group_2	0.067
r_ncsr_local_group_4	0.065
r_ncsr_local_group_1	0.059
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6548
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	15

Software

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