8PIO | pdb_00008pio

Crystal structure of Ser33 in complex with PHP (3-phosphohydroxypyruvate)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M SPG pH=6 25 % w/v PEG 1500 7.4 mg/ml of protein in 25 mM Tris pH=7.5 and 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.6	α = 69.84
b = 95.15	β = 88.72
c = 108.37	γ = 85.65

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 PILATUS3 6M		2021-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

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	2.6	52.04	97.87	0.992	9.82	5.1		68361

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	2.6	2.693			0.604	1.09

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YBA	2.6	52.04	64884	3369	97.93	0.22431	0.22237	0.2226	0.2617	0.2615	RANDOM	70.671

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]
1.29	6.11	-1.3	1.77	1.68	-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.518
r_dihedral_angle_4_deg	18.987
r_dihedral_angle_3_deg	13.786
r_long_range_B_refined	10.996
r_long_range_B_other	10.995
r_mcangle_it	8.387
r_mcangle_other	8.386
r_scangle_other	8.34
r_dihedral_angle_1_deg	6.151
r_mcbond_other	5.663
r_mcbond_it	5.662
r_scbond_it	5.548
r_scbond_other	5.545
r_angle_other_deg	1.151
r_angle_refined_deg	1.132
r_chiral_restr	0.035
r_bond_refined_d	0.007
r_bond_other_d	0.004
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12946
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	244

Software

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