8B6U | pdb_00008b6u

Mpf2Ba1 monomer

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QP2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M MgCl2 hexahydrate 0.1M HEPES pH=7.5 30% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
4.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.6	α = 90
b = 127.6	β = 90
c = 116.12	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

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	2.13	71.25	99.5	0.104	10.8	4.6		53473

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.25			0.707

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	2QP2	2.134	57.13	53424	2602	99.29	0.211	0.2094	0.22	0.2414	0.24	31.264

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]
0.029			0.029		-0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.175
r_dihedral_angle_6_deg	17.136
r_dihedral_angle_2_deg	9.948
r_dihedral_angle_1_deg	9.406
r_lrange_it	7.156
r_lrange_other	7.143
r_scangle_it	5.678
r_scangle_other	5.677
r_mcangle_other	4.415
r_mcangle_it	4.414
r_scbond_it	3.921
r_scbond_other	3.92
r_mcbond_it	3.116
r_mcbond_other	3.11
r_angle_refined_deg	1.86
r_angle_other_deg	0.658
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.219
r_symmetry_nbd_other	0.204
r_nbd_other	0.202
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.145
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3730
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing