22OC | pdb_000022oc

Crystal structure of P210 CD lyase

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, HANGING DROP	8	291	0.1 M Tris pH 8.0,1.6 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.67	α = 90
b = 109.67	β = 90
c = 51.38	γ = 120

Symmetry
Space Group	H 3

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 PILATUS3 6M		2025-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2	27.433	99.9	0.047	0.06	0.036	0.999	19.4	5.1		15540

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.3	0.374	0.22	0.932

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	2	27.433	15540	738	99.852	0.163	0.1615	0.1707	0.2	0.2067	25.09

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]
0.071	0.035		0.071		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.963
r_dihedral_angle_3_deg	11.039
r_lrange_it	6.84
r_lrange_other	6.811
r_dihedral_angle_1_deg	6.611
r_scangle_it	5.456
r_scangle_other	5.347
r_dihedral_angle_2_deg	4.892
r_scbond_it	3.619
r_scbond_other	3.56
r_mcangle_it	3.177
r_mcangle_other	3.176
r_mcbond_it	2.199
r_mcbond_other	2.188
r_angle_refined_deg	1.576
r_angle_other_deg	0.564
r_nbd_refined	0.203
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbd_refined	0.128
r_nbd_other	0.104
r_metal_ion_refined	0.095
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.075
r_ext_dist_refined_b	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1528
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing