8ZLF | pdb_00008zlf

Crystal structure of DH domain of FYVE Domain containing protein(FP10) from Entamoeba histolytica

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		289.15	1.5M Sodium Citrate tribasic dihydrate, 0.1M Sodium Citrate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.59	α = 90
b = 69.337	β = 118.275
c = 57.615	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 EIGER X 16M		2021-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	2.48	50.741	90.4	0.99	2.6	7.1		16337

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	2.48	5.544			0.93

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	2.48	50.741	12690	697	90.404	0.237	0.2339	0.2355	0.2893	0.2855	39.861

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]
-4.04		-1.922	6.717		-0.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.102
r_dihedral_angle_6_deg	15.331
r_dihedral_angle_2_deg	11.925
r_lrange_it	11.517
r_lrange_other	11.516
r_scangle_other	8.164
r_scangle_it	8.162
r_mcangle_it	6.743
r_mcangle_other	6.743
r_dihedral_angle_1_deg	6.44
r_scbond_it	5.263
r_scbond_other	5.253
r_mcbond_it	4.465
r_mcbond_other	4.465
r_angle_refined_deg	1.423
r_angle_other_deg	0.486
r_nbd_other	0.324
r_symmetry_nbd_refined	0.289
r_nbd_refined	0.247
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.158
r_ncsr_local_group_1	0.126
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.007
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	3037
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
BALBES	phasing