8QKR

Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.251

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.3M Calcium chloride 0.1M Magnesium formate HCl 22.5% (v/v) PurePEGs Cocktail

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.927	α = 60.535
b = 92.016	β = 72.132
c = 92.492	γ = 79.818

Symmetry
Space Group	P 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 EIGER2 XE 16M		2023-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	3.13	59.104	98.6	0.955	0.405	3.7		30110

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	3.23	3.29			0.245

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.234	59.104	30108	1403	98.54	0.257	0.2536	0.3268	71.736

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]
0.118	0.872	3.203	3.125	0.102	-0.734

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.774
r_lrange_other	14.729
r_lrange_it	14.725
r_dihedral_angle_6_deg	13.271
r_mcangle_other	9.641
r_mcangle_it	9.638
r_dihedral_angle_1_deg	9.171
r_scangle_it	8.636
r_scangle_other	8.635
r_dihedral_angle_2_deg	5.99
r_mcbond_it	5.816
r_mcbond_other	5.811
r_scbond_it	5.008
r_scbond_other	5.008
r_angle_refined_deg	1.397
r_angle_other_deg	0.501
r_xyhbond_nbd_refined	0.258
r_nbd_refined	0.251
r_nbd_other	0.219
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.189
r_ncsr_local_group_3	0.176
r_ncsr_local_group_1	0.139
r_symmetry_nbd_refined	0.133
r_ncsr_local_group_2	0.128
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11728
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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