7YDT | pdb_00007ydt

Crystal structure of mouse MPND

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PBD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG4000, Bis Tris, ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.677	α = 90
b = 62.838	β = 90
c = 112.619	γ = 90

Symmetry
Space Group	P 21 2 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 2M		2020-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9793	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	50	97.6	0.098	13.3	5.8		17365

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	2.05	2.1			0.883

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	6PBD	2.055	41.971	16909	885	97.419	0.231	0.2296	0.23	0.2495	0.26	34.645

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]
-1.293			-2.73		4.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.557
r_dihedral_angle_3_deg	14.324
r_dihedral_angle_4_deg	12.337
r_dihedral_angle_1_deg	5.513
r_lrange_it	3.725
r_lrange_other	3.693
r_scangle_it	2.092
r_scangle_other	2.091
r_mcangle_it	2.081
r_mcangle_other	2.079
r_mcbond_it	1.22
r_mcbond_other	1.22
r_scbond_it	1.202
r_scbond_other	1.201
r_angle_refined_deg	1.149
r_angle_other_deg	1.091
r_nbd_refined	0.169
r_nbd_other	0.162
r_symmetry_nbd_other	0.161
r_symmetry_xyhbond_nbd_refined	0.16
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.124
r_symmetry_nbd_refined	0.109
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1427
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing