6C2W

Crystal structure of human prothrombin mutant S101C/A470C

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EDM	5EDM and 3NXP
experimental model	PDB	3NXP	5EDM and 3NXP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	277	100 mM Bicine, pH 9.0 and 11% PEG 3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.03	α = 105.35
b = 85.074	β = 90
c = 153.801	γ = 90.05

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	IMAGE PLATE	RIGAKU RAXIS IV++		2017-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	4.1	40	91.7	0.156	5.7	2.5		30018	-1	-1

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	4.1	4.17	74.1		0.675		1.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5EDM and 3NXP	4.12	30.32	26884	1394	88.04	0.28085	0.27826	0.33298	RANDOM	191.324

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]
33.56	-6.84	51.31	20.54	14.49	-54.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.082
r_long_range_B_refined	21.73
r_long_range_B_other	21.729
r_dihedral_angle_3_deg	15.765
r_mcangle_it	14.908
r_mcangle_other	14.907
r_scangle_other	11.479
r_dihedral_angle_4_deg	10.358
r_mcbond_it	8.852
r_mcbond_other	8.848
r_dihedral_angle_1_deg	6.673
r_scbond_it	6.628
r_scbond_other	6.62
r_angle_refined_deg	1.177
r_angle_other_deg	0.917
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	9188
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing