9S7K | pdb_00009s7k

INCYPRO crosslinked dimer of the D-stereospecific hydrolase dHy1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure of APO DHy

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	100 mM MES/Imidazole pH 7, 13 %(v/v) PEG-20000, 26 %(w/v) PEG550-MME, 0.1 M Morpheus Carboxylic Acids

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.776	α = 75.692
b = 53.764	β = 75.693
c = 57.373	γ = 87.81

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER2 XE 16M		2024-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.771	43.115	91.8	0.034	0.999	11.8	6.9		35659		1.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.771	1.967	56.7		0.509	0.49	1.4	6.6

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	FREE R-VALUE	1.771	43.115	35658	1752	60.746	0.241	0.2399	0.2427	0.2696	0.273	43.221

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]
25.97	-6.572	-6.465	-20.958	6.185	-5.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.814
r_dihedral_angle_3_deg	12.582
r_dihedral_angle_6_deg	11.552
r_dihedral_angle_1_deg	6.741
r_lrange_it	3.142
r_lrange_other	3.132
r_mcangle_it	1.553
r_mcangle_other	1.553
r_dihedral_angle_other_2_deg	1.254
r_scangle_it	1.049
r_scangle_other	1.049
r_angle_refined_deg	0.886
r_mcbond_it	0.835
r_mcbond_other	0.835
r_scbond_it	0.532
r_scbond_other	0.532
r_angle_other_deg	0.347
r_symmetry_xyhbond_nbd_refined	0.176
r_symmetry_nbd_other	0.175
r_nbd_refined	0.173
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_nbd_other	0.122
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.044
r_ncsr_local_group_1	0.026
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5194
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing
Coot	model building