8WLX | pdb_00008wlx

Crystal structure of P123A_Msd

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XKO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1M MES pH 6.4, 0.2M Mg-acetate tetrahydrate, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.66	α = 90
b = 108.56	β = 90
c = 53.19	γ = 90

Symmetry
Space Group	P 21 21 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		2021-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	1.56	19.763	100	0.99	16.79	12.5		53097

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	1.562	1.602			0.83

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	1.562	19.763	53016	967	99.896	0.171	0.1703	0.1829	0.1932	0.2053	18.634

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]
-0.006			-0.023		0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.976
r_dihedral_angle_3_deg	11.759
r_dihedral_angle_2_deg	9.213
r_dihedral_angle_1_deg	5.809
r_lrange_it	5.732
r_lrange_other	5.671
r_scangle_it	4.518
r_scangle_other	4.517
r_scbond_it	3.063
r_scbond_other	3.062
r_mcangle_other	2.465
r_mcangle_it	2.46
r_angle_refined_deg	1.746
r_mcbond_it	1.653
r_mcbond_other	1.632
r_angle_other_deg	0.664
r_symmetry_xyhbond_nbd_refined	0.257
r_nbd_refined	0.22
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.181
r_nbd_other	0.155
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.133
r_metal_ion_refined	0.116
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2390
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing