9GPH | pdb_00009gph

Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (-1) and phosphate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		285	to be retrieved

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.386	α = 90
b = 67.57	β = 90
c = 299.54	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		2018-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.03987	ESRF	ID29

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	1.7	50.005	99.5	0.971	2	3.6		150586

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	1.7	1.79			0.731

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	1.7	50.005	150434	7453	99.349	0.193	0.1919	0.203	0.2157	0.2253	23.233

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]
1.513			0.785		-2.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.459
r_dihedral_angle_3_deg	11.735
r_dihedral_angle_1_deg	7.688
r_dihedral_angle_2_deg	7.495
r_lrange_it	5.623
r_lrange_other	5.553
r_scangle_it	4.647
r_scangle_other	4.647
r_scbond_it	3.049
r_scbond_other	3.048
r_mcangle_it	2.624
r_mcangle_other	2.624
r_mcbond_it	1.945
r_mcbond_other	1.944
r_angle_refined_deg	1.521
r_angle_other_deg	0.532
r_nbd_refined	0.192
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.172
r_nbd_other	0.164
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_5	0.084
r_chiral_restr	0.082
r_ncsr_local_group_6	0.082
r_ncsr_local_group_2	0.081
r_ncsr_local_group_1	0.077
r_ncsr_local_group_4	0.065
r_ncsr_local_group_3	0.059
r_xyhbond_nbd_other	0.022
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9752
Nucleic Acid Atoms
Solvent Atoms	809
Heterogen Atoms	96

Software

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