1ZRH

Crystal structure of Human heparan sulfate glucosamine 3-O-sulfotransferase 1 in complex with PAP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	300	2.0 - 2.4 M Sodium Formate, 0.1 M Sodium-Acetate pH 4.6, 5% Glycerol, VAPOR DIFFUSION, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.887	α = 90
b = 135.255	β = 90
c = 48.21	γ = 90

Symmetry
Space Group	P 21 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	VariMax	2005-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.1	67.57	98.5	0.114	0.114	8.5	5.1	22876	22876			25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.17	98.1		0.551	0.551	3.04	4.9	2235

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VKJ	2.1	67.57	22105	22105	741	98.38	0.1849	0.1849	0.18408	0.19	0.20911	0.21	RANDOM	22.827

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]
0.05			-0.87		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.089
r_dihedral_angle_4_deg	17.838
r_dihedral_angle_3_deg	14.839
r_dihedral_angle_1_deg	5.914
r_scangle_it	4.317
r_scbond_it	2.915
r_mcangle_it	1.857
r_angle_refined_deg	1.689
r_mcbond_it	1.212
r_symmetry_hbond_refined	0.442
r_nbtor_refined	0.308
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.187
r_symmetry_vdw_refined	0.183
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2207
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	27

Software

Software
Software Name	Purpose
CrystalClear	data collection
SCALEPACK	data scaling
PHASES	phasing
REFMAC	refinement
CrystalClear	data reduction