8ZLC | pdb_00008zlc

Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum

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	0.2M Ammonium Acetate, 25% PEG 3350, 0.1M bis-tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.377	α = 90
b = 62.742	β = 90
c = 91.784	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 EIGER2 X 9M		2023-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	2.13	51.8	99.94	0.994	5.35	4.82		18741

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	2.13	2.185			0.732

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	2.13	51.797	14249	711	99.853	0.187	0.1847	0.1956	0.2287	0.2136	27.033

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]
-1.195			0.939		0.256

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.174
r_dihedral_angle_3_deg	16.752
r_dihedral_angle_4_deg	11.744
r_dihedral_angle_1_deg	6.6
r_lrange_it	6.251
r_lrange_other	6.244
r_scangle_it	4.928
r_scangle_other	4.928
r_mcangle_it	3.209
r_mcangle_other	3.208
r_scbond_it	3.1
r_scbond_other	3.099
r_mcbond_it	2.143
r_mcbond_other	2.14
r_angle_refined_deg	1.539
r_angle_other_deg	1.313
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.2
r_nbd_other	0.195
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.145
r_ncsr_local_group_1	0.13
r_symmetry_xyhbond_nbd_other	0.101
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2103
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms

Software

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