8AMT | pdb_00008amt

OBD-RepB pMV158 domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.1 M Tri-sodium citrate pH 5.0 1M LiCl 30 % PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.45	α = 90
b = 48.15	β = 90
c = 73.75	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		2016-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

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	1.5	32.66	99.8	0.186	9.1	13.4		26009

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	1.5	32.66			1.387	0.023

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	3DKX	1.5	32.682	25957	1287	99.674	0.156	0.1554	0.16	0.1746	0.18	12.903

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			0.114		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.83
r_dihedral_angle_4_deg	27.7
r_dihedral_angle_3_deg	11.365
r_dihedral_angle_1_deg	6.527
r_lrange_other	5.373
r_lrange_it	5.371
r_scangle_it	3.866
r_scangle_other	3.864
r_scbond_it	2.516
r_scbond_other	2.515
r_mcangle_other	2.195
r_mcangle_it	2.178
r_angle_refined_deg	1.905
r_angle_other_deg	1.483
r_mcbond_it	1.414
r_mcbond_other	1.384
r_nbd_refined	0.224
r_nbd_other	0.186
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.085
r_symmetry_nbd_refined	0.084
r_bond_refined_d	0.014
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	1056
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
pointless	data scaling
PHASER	phasing