8PPS | pdb_00008pps

Dimeric RbdA EAL, in apo state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	294.15	100mM Tris and BICINE pH 9 34% (w/v) ethylene glycol and PEG 8000 mix

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.4	α = 90
b = 65.72	β = 90
c = 172.25	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 PILATUS 6M		2017-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9789	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.3	46.04	93.5	0.059	0.999	15.9	4.6		31120			60.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	78		0.918	0.665	1.32	3.1

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	2.3	46.04	31120	1495	93.496	0.186	0.1839	0.19	0.2324	0.23	58.816

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]
3.679			-1.625		-2.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.036
r_dihedral_angle_6_deg	15.899
r_lrange_other	10.317
r_lrange_it	10.307
r_dihedral_angle_2_deg	9.405
r_scangle_it	8.478
r_scangle_other	8.477
r_mcangle_it	6.122
r_mcangle_other	6.121
r_dihedral_angle_1_deg	6.084
r_scbond_it	5.776
r_scbond_other	5.775
r_mcbond_it	4.19
r_mcbond_other	4.19
r_angle_refined_deg	1.551
r_angle_other_deg	0.531
r_symmetry_nbd_refined	0.266
r_nbd_other	0.237
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.159
r_ncsr_local_group_1	0.13
r_metal_ion_refined	0.113
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.074
r_bond_refined_d	0.009
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	3957
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building