4O03 | pdb_00004o03

Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NZQ	PDB entry 4NZQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	100 mM HEPES, pH 7.5, 10% PEG 4000 and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.92	75.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.459	α = 90
b = 89.431	β = 116.36
c = 87.982	γ = 90

Symmetry
Space Group	C 1 2 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++		2013-06-28	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	3.38	40	95.8	0.128	6.9	2.9	17364	16635	-0.7	-0.7

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	3.38	3.46	92.4		0.43	2	2.1	805

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	PDB entry 4NZQ	3.38	39.75	-0.7	-0.7	16638	15753	835	94.68	0.23539	0.23299	0.2317	0.27942	0.2758	RANDOM	73.096

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]
0.22			-0.05		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.199
r_dihedral_angle_3_deg	23.777
r_dihedral_angle_4_deg	20.261
r_dihedral_angle_1_deg	8.397
r_scangle_it	2.04
r_angle_refined_deg	1.65
r_mcangle_it	1.196
r_scbond_it	1.148
r_mcbond_it	0.639
r_chiral_restr	0.113
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4321
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	47

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling