9S8W | pdb_00009s8w

Human heparanase in complex with neutralizing antibody A54 Fab fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E8M	heparanase
experimental model	PDB	1AE6	fab fragment

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Nitrate 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.738	α = 90
b = 69.738	β = 90
c = 429.781	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	PIXEL	DECTRIS EIGER X 9M		2019-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91589	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	3.49	107.44	86.8	0.28	0.999	9.2	15		9227

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.49	3.87			2.25	0.95	1.7

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	3.49	107.44	9227	465	63.446	0.224	0.2197	0.2185	0.323	0.3212	143.262

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]
-0.237			-0.237		0.475

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.776
r_dihedral_angle_6_deg	15.647
r_lrange_it	11.558
r_lrange_other	11.557
r_dihedral_angle_1_deg	6.65
r_scangle_it	5.684
r_scangle_other	5.684
r_mcangle_it	4.764
r_mcangle_other	4.763
r_scbond_it	3.238
r_scbond_other	3.238
r_dihedral_angle_2_deg	3.139
r_mcbond_it	2.76
r_mcbond_other	2.76
r_angle_refined_deg	1.813
r_angle_other_deg	0.628
r_nbd_other	0.27
r_symmetry_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.21
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.085
r_ext_dist_refined_b	0.079
r_symmetry_xyhbond_nbd_other	0.019
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	6983
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
MOLREP	phasing