1X9D

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FMI	PDB ENTRY 1FMI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.687	α = 89.49
b = 53.878	β = 63.6
c = 56.234	γ = 62.61

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.99985	APS	22-ID

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	1.41	50	95.5	0.102				84600

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)
	1.41	1.46	93.2		0.129

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FMI	1.41	48.8	76092	8507	95.45	0.146	0.14598	0.144	0.162	RANDOM	8.368

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]
0.26	-0.25	-0.02	-0.07	0.02	0.05

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES, PERIOD 2 (DEGREES)	32.283
TORSION ANGLES, PERIOD 4 (DEGREES)	13.33
r_dihedral_angle_2_deg	11.599
r_dihedral_angle_1_deg	5.907
r_scangle_it	3.505
r_scbond_it	2.439
r_mcangle_it	2.257
r_mcbond_it	1.717
r_angle_refined_deg	1.337
r_angle_other_deg	0.826
MAIN-CHAIN BOND OTHER ATOMS (A**2)	0.499
r_symmetry_vdw_other	0.24
r_nbd_refined	0.22
NON-BONDED TORSION REFINED ATOMS (A)	0.184
r_nbd_other	0.167
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.087
r_nbtor_other	0.082
r_symmetry_hbond_refined	0.069
POTENTIAL METAL-ION REFINED ATOMS (A)	0.045
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3668
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
EPMR	phasing