8I34

The crystal structure of EPD-BCP1 from a marine sponge

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		296	2-Amino-2-(hydroxymethyl)propane-1,3-diol, magnesium chloride, polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.749	α = 90
b = 101.38	β = 95.06
c = 112.588	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 S 6M		2022-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	2.44	75.32	99.9	0.104	0.125	0.068	0.981	7	3.3		61509			36.8

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	2.44	2.5	99.7		0.584	0.702	0.385	0.746	1.8	3.2

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	FREE R-VALUE	AlphaFold	2.44	75.32	61486	2954	99.891	0.204	0.2015	0.21	0.2482	0.26	43.642

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]
4.431		1.587	-2.54		-2.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.711
r_dihedral_angle_3_deg	14.773
r_lrange_it	8.97
r_lrange_other	8.97
r_dihedral_angle_1_deg	7.986
r_scangle_it	6.654
r_scangle_other	6.653
r_mcangle_it	6.636
r_mcangle_other	6.636
r_dihedral_angle_2_deg	5.992
r_scbond_it	4.348
r_scbond_other	4.347
r_mcbond_it	4.311
r_mcbond_other	4.309
r_angle_refined_deg	1.403
r_angle_other_deg	0.489
r_xyhbond_nbd_refined	0.306
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.207
r_symmetry_nbd_other	0.196
r_nbd_other	0.194
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_refined	0.066
r_chiral_restr	0.064
r_ncsr_local_group_5	0.042
r_ncsr_local_group_7	0.042
r_ncsr_local_group_8	0.04
r_ncsr_local_group_6	0.039
r_ncsr_local_group_2	0.036
r_ncsr_local_group_3	0.036
r_ncsr_local_group_9	0.035
r_ncsr_local_group_12	0.035
r_ncsr_local_group_1	0.033
r_ncsr_local_group_10	0.031
r_ncsr_local_group_4	0.029
r_ncsr_local_group_11	0.022
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10660
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	687

Software

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