7ZS6 | pdb_00007zs6

Crystal structure of Apis mellifera RidA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ONI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2 M Magnesium chloride hexahydrate, 0.1 M MES, 20% PEG 6000 pH 6

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.499	α = 90
b = 109.499	β = 90
c = 141.092	γ = 90

Symmetry
Space Group	I 41 2 2

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		2020-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.31	43.305	99.44	0.033	0.999	14.8	4.4		101696

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.33			1.236	0.404

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1ONI	1.31	43.305	101696	5097	99.381	0.132	0.1305	0.13	0.1644	0.17	23.816

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]
0.032			0.032		-0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.167
r_dihedral_angle_4_deg	18.613
r_dihedral_angle_3_deg	13.405
r_dihedral_angle_1_deg	6.963
r_scangle_it	5.058
r_scangle_other	5.055
r_scbond_it	4.629
r_scbond_other	4.629
r_lrange_it	4.579
r_lrange_other	4.479
r_rigid_bond_restr	4.323
r_mcangle_other	3.051
r_mcangle_it	3.047
r_mcbond_it	2.778
r_mcbond_other	2.748
r_angle_refined_deg	2.059
r_angle_other_deg	1.485
r_nbd_refined	0.239
r_nbd_other	0.234
r_xyhbond_nbd_refined	0.231
r_symmetry_nbd_refined	0.189
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.142
r_chiral_restr	0.115
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3105
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MoRDa	phasing