5EDM

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O03	PDB CODE 4O03

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES, pH 6.5 and 1.6 M MgSO4

Crystal Properties
Matthews coefficient	Solvent content
5.16	73.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.884	α = 90
b = 168.69	β = 90
c = 144.315	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2014-08-14	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	2.2	92.07	98	0.087	17	7.3		67055		-0.3

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	2.2	2.24	97.8		0.487	3	4.4

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	PDB CODE 4O03	2.2	92.07	63362	3409	98	0.198	0.196	0.236	RANDOM	59.17

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]
-0.78			-1.2		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.131
r_dihedral_angle_4_deg	16.922
r_dihedral_angle_3_deg	16.169
r_long_range_B_refined	9.711
r_long_range_B_other	9.627
r_dihedral_angle_1_deg	6.623
r_scangle_other	4.728
r_scbond_it	3.603
r_scbond_other	3.497
r_mcangle_it	2.824
r_mcangle_other	2.824
r_mcbond_it	1.706
r_mcbond_other	1.706
r_angle_refined_deg	1.681
r_angle_other_deg	0.812
r_chiral_restr	0.116
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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	4414
Nucleic Acid Atoms
Solvent Atoms	464
Heterogen Atoms	138

Software

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