8IZ2 | pdb_00008iz2

Single excitation and two emissions pH sensor protein (SITE-pHorin)_C203E_pH8.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	PEG 8000, MgCl2, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.2	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.024	α = 90
b = 62.896	β = 90
c = 67.59	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 PILATUS3 6M		2018-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.57	50	99.4	0.083	0.024	38	12.8		32699

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.6	87.9		0.35	0.108	5.78	10.9

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	1.572	42.236	32615	1619	99.758	0.161	0.1595	0.1726	0.1803	0.1941	18.003

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]
-0.009			-0.002		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.493
r_dihedral_angle_4_deg	15.39
r_dihedral_angle_3_deg	12.1
r_dihedral_angle_1_deg	7.075
r_lrange_it	6.046
r_lrange_other	5.92
r_scangle_it	5.018
r_scangle_other	5.016
r_scbond_it	3.274
r_scbond_other	3.273
r_mcangle_other	2.377
r_mcangle_it	2.376
r_angle_refined_deg	1.797
r_mcbond_it	1.653
r_mcbond_other	1.649
r_angle_other_deg	1.574
r_nbd_other	0.312
r_symmetry_nbd_refined	0.271
r_nbd_refined	0.209
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_other	0.117
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1818
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing