9WVZ | pdb_00009wvz

crystal structure of retro-aldolase T53L/K210H RA95.5-8 with a covalently bound cyclohexenone derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PA8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	0.2 M ( NH4)2SO4, 0.1M MES pH6.5, 30% v/v PEG 5000 MME.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.75	α = 90
b = 69.171	β = 90
c = 69.51	γ = 90

Symmetry
Space Group	P 21 21 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	DECTRIS EIGER X 16M		2025-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	1	SSRF	BL10U2

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	1.79	50	98.5	0.995	24.7	8.9		28483

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	1.79	1.85			0.977

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 (Observed)	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	1.79	49.03	27028	1406	98.25	0.17608	0.1742	0.1885	0.21229	0.2196	RANDOM	30.239

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]
-0.83			-0.06		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.331
r_dihedral_angle_4_deg	15.322
r_dihedral_angle_3_deg	13.351
r_long_range_B_other	8.736
r_long_range_B_refined	8.731
r_scangle_other	7.165
r_dihedral_angle_1_deg	6.031
r_scbond_other	4.823
r_scbond_it	4.822
r_mcangle_it	4.101
r_mcangle_other	4.1
r_mcbond_it	3.045
r_mcbond_other	3.042
r_angle_refined_deg	1.892
r_angle_other_deg	1.588
r_chiral_restr	0.253
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1975
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing