Experiment: 5YQB

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	2.0M Sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.92

Symmetry
Space Group	P 31 2 1

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++		2016-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	98.6	0.035	0.039	0.016	0.999	24	4.7		198652			22.44

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.62	100		0.337	0.381	0.17	0.906	4.37	4.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HPO	1.56	50	187925	9844	98.16	0.16239	0.16136	0.18189	RANDOM	23.628

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.053
r_dihedral_angle_4_deg	16.407
r_dihedral_angle_3_deg	12.239
r_long_range_B_refined	6.212
r_long_range_B_other	6.096
r_dihedral_angle_1_deg	6.076
r_scangle_other	5.474
r_scbond_it	3.814
r_scbond_other	3.811
r_angle_refined_deg	2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.053
r_dihedral_angle_4_deg	16.407
r_dihedral_angle_3_deg	12.239
r_long_range_B_refined	6.212
r_long_range_B_other	6.096
r_dihedral_angle_1_deg	6.076
r_scangle_other	5.474
r_scbond_it	3.814
r_scbond_other	3.811
r_angle_refined_deg	2.6
r_mcangle_it	2.36
r_mcangle_other	2.36
r_angle_other_deg	2.112
r_mcbond_it	1.802
r_mcbond_other	1.801
r_chiral_restr	0.17
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6940
Nucleic Acid Atoms
Solvent Atoms	869
Heterogen Atoms	42